CLC Genomics Workbench Changelog

What's new in CLC Genomics Workbench 9.5.2

Oct 25, 2016

Improvements:
SRA download functionality has been updated to support the upcoming NCBI transition to HTTPS.
Updated the restriction enzyme list from REBASE.
Bug fixes:
Fixed a bug where running two or more concurrent instances of RNA-Seq Analysis with EM quantification could in some cases lead to incorrect results or error messages.
Fixed an issue with running BLAST on macOS Sierra.
Updated PFAM links reported by the Pfam Domain Search tool.
Fixed an issue introduced in CLC Genomics Workbench 9.5 where enzymes listed alphabetically after RdeGBI were missing methylation information.
Various minor bugfixes.
Advanced Notice:
The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.
Support for some older operating systems (OS), listed below, will be discontinued in early 2017. Software released at that time and later may still run without issue, but problems experienced due to using an unsupported OS will not be addressed. If you are concerned about the proposed change, please contact our Support team ([email protected]), letting them know the OS being used and the products you are running on that OS.

New in CLC Genomics Workbench 9.5.1 (Sep 29, 2016)

New in CLC Genomics Workbench 9.5 (Sep 17, 2016)

NEW TOOLS:
"Search for Reads in SRA..." allows search and download of reads from the SRA database. Its is available from the Download button.
A new GFF3 importer is available as an option in the Import -> Tracks tool.
"Identify Known Mutations from Sample Mapping" can be used to look up known genomic variants in read mappings. Available from the "Resequencing Analysis" tool folder.
"Identify Candidate Variants" can be used to identify and extract variants that fulfill certain criteria. Available from the "Annotate and Filter Variants" tool folder.
A new option "Use EM estimation (recommended)" was added to the RNA-Seq Analysis tool. This enables the use of an expectation-maximization algorithm to distribute ambiguous reads between isoform/genes.
IMPROVEMENTS:
Resequencing:
The Local Realignment tool has a new option that can allow the use of guidance variants longer than 100bp.
The InDels and Structural Variants tool now offers the option to include reads mapped as broken pairs in the analysis.
The InDels and Structural Variants tool offers now the option for consensus calculation to ignore reads if their relative coverage or quality scores are too low.
The COSMIC importer has been updated to support the latest version of the COSMIC database, release v77.
Improved performance of a number of tools when run on systems with multiple cores: Annotate from Known Variants, Filter against Known Variants, Filter against Control Reads, Annotate with Exon Numbers, Annotate with Flanking Sequences, Filter Marginal Variant Calls, Filter Reference Variants, Compare Sample Variant Tracks, Trio Analysis, GO Enrichment Analysis, Amino Acid Changes, Annotate with Conservation Score, Predict Splice Site Effect, Link Variants to 3D Protein Structure, Merge Annotation Tracks, Create Statistics for Target Regions, and Fisher Exact Test.
RNA-Seq:
The tools "Filter Based On Overlap" and "Annotate with Overlap Information" now work with the Statistical Comparison Tracks produced by the Advanced RNA-Seq plugin.
It is now possible to export expression tracks in BED format. The expression value will be exported as the score.
Expression tracks are now colored according to a log-scale to ease visual interpretation of expression data.
The track view of expression tracks dynamically rescales to make best use of the screen real estate. This change brings expression tracks in line with other track types.
Launch:
The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.
Analyses can now be launched on data elements listed in the results table of a Local Search by selecting the elements of interest, right clicking with the mouse and navigating through the context menu that appears.
Workflows:
Workflow outputs can now be configured so that subfolders to contain the outputs are created.
New placeholders are available when defining the names of workflow outputs: {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour}, {minute}, {second}.
Placeholders within workflow output names that were previously available only as digits can now be specified using written names: {name} is a synonym for {1} and {input} is a synonyms for {2}.
When using the {2} placeholder for custom naming in workflow output elements, only unlocked inputs will be included in the generated name.
In the generated pdf showing all the configured parameters of a workflow, entries for parameters connected to a tool or an input element now list the names of the defining elements. Previously the parameter listings for such elements were left blank.
The History view of data elements created using a workflow now includes information about the workflow that created them.
Where a tool name has been altered in a workflow, the original name is now included alongside the changed name when exporting workflow parameters.
The order of the tools in the workflow "Add Element" menu now matches the order in the Workbench Toolbox menu.
Metadata:
A "Remove Association(s)" option for removing metadata associations from selected data elements has been added sin the Metadata Elements view in a right click context menu.
In the Metadata Find Associated Data view it is now also possible to use Find in Navigation Area when multiple rows are selected.
When importing metadata from a spreadsheet with formulas in it, the result of the evaluation of the formula (as displayed in Excel) is now imported rather than the formula itself.
Improved workflow validation to aid the user in identifying inputs that will be ignored due to the configuration of the workflow elements.
General:
The Trim Sequences tool under Toolbox | NGS Core Tools now handles ambiguity codes in the adapter/primer sequences.
The upper limit for the "discard reads above length" option of the Trim Sequences tool under Toolbox | NGS Core Tools has been raised from 8000 to 99,999.
The Identify Graph Thresholds tool can now be configured to work on specified regions only.
A new option in the Sample Reads tool makes it possible to choose whether sampling should be deterministic or random.
The "Sort folder" tool now uses numerical sorting for filenames prefixed with a number.
New placeholders are available when defining the names of exporter outputs: {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}.
Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.
The Identify Graph Thresholds tool can now be run using only a lower or upper threshold limit, rather than having to specify both.
The Extract Consensus Sequence tool now outputs a sequence list for all results. Previously, when running this tool directly, if the result was a single sequence, it would output a sequence, not a sequence list. (Nothing has changed when this tool is run as part of a workflow, where sequence lists were always generated).
The Extract Consensus Sequence tool no longer displays a message bubble after each contig has been processed.
The Download Reference Genome Data manager now shows version numbers for several genome annotations.
The list of enzymes pre-installed in the workbench has been updated from REBASE.
Read group details are now shown on the Element Info view of sequence lists.
The "Unknown" feature category can now be hidden in tree editors.
The option "is not in list" has been introduced as a new table filtering option.
All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
GenBank import now also allows for file names with 'GBFF' extension.
Standard deviations in reports are now being calculated with a different algorithm than previously. This will have no noticeable effect in the overwhelming majority of cases.
The History view of variant, feature and expression tracks that are created by pressing the "Create Track from Selection" button on the table view of an existing track will now include details of any advanced filtering that was applied to the table at the time the new track was made.
Three prime UTR and five prime UTR tracks from the "Download Reference Genome Data" tool are now named with distinct suffices. Previously the track names ended with ""_utr" and ""_utr-1".
Improved the progress reporting for the import of large, gzip compressed Illumina and Ion-Torrent files.
General speed and usability improvements.
CHANGES:
Retirements:
The Expression Profiling by Tags folder has been moved to the Legacy Tools section of the toolbox
Bug fixes:
Fixed an issue with the tools "Extract from Selection" and "Extract Reads Based on Overlap" so that they now correctly extract mapped reads that extend over the (arbitrarily chosen) ends of the 1D representation of a circular genome.
Fixed an issue where the Motif Search tool was incorrectly reporting all match accuracies as either 0% or 100%.
Fixed an issue that caused characters in sequence names to be rendered incorrectly when a report was exported to Excel.
The Download Reference Genome Data manager will now always refer to the latest version of the Ensembl GRCh38 Genome. It was previously locked to Ensembl version 82.
Fixed an issue where, when searching for both read1 and read2 in a broken pair, the "Find Broken Pair Mates" tool reported that the mate of read1 was itself. The tool now correctly shows that the mate of read1 is read2.
The Create New Sequence List button in a broken pair table now works when multiple read groups are involved.
Fixed an issue that would make the wizard for the Demultiplex Reads tool fail if an invalid bar code was entered.
Fixed a bug that made graphics export of some plots from reports fail.
Fixed a rarely occurring bug where rendering of a Read Mapping in a Track List would fail.
The Find Binding Sites and Create Fragments tools now properly display mismatches when the primer input is in lower-case.
Fixed an issue where, when viewing statistical comparison tracks together with read mapping tracks, the statistical comparison track annotations could sometimes be rendered as offset from their true genomic positions.
Fixed a memory leak in the Extract Consensus Sequence tool.
Fixed an issue where sequences of length zero would cause the Create BLAST Database tool to throw an error. Such sequences are now skipped and will not included in the final database.
The Illumina High-Throughput Sequencing Import tool now correctly warns that zip files with multiple entries are not supported.
Tables with more than 126 million entries now show a warning that they contain too much data to display instead of leaving the table empty.
Fixed an issue in the wizard for the tool Create Entry Clone where a previously used data located on an unmounted location would result in an error message being shown.
Fixed an issue where right-clicking on a graph in a report and choosing to show "Report", "History" or "Element Info" triggered an error.
Fixed an issue where it took a long time to open a workbench it it was previously closed when displaying an open table editor that had been sorted.
Fixed a bug in the "Manage Enzymes" wizard that prevented a user from cancelling the action if "Save as new enzyme list" was enabled.
Fixed a rare issue where some annotations could, but did not necessarily, go missing on sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option "Delete selection" was used.
Fixed an issue with links in tables to the PDB and dbEST databases.
Fixed a rare issue that caused the "Extract from selection" right-click option not to work for a reads track in a track list.
Fixed a bug where exporting to Wiggle on systems with specific system locales would produce files that could not be re-imported.
Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.
Fixed an issue affecting the launching of workflows with multiple inputs in batch, where the workflow execution wizard did not update correctly when another metadata spreadsheet was selected.
Fixed an issue where, when the Processes tab was hidden and then shown again, any processes listed before the tab was hidden were no longer shown.
Fixed an issue where the save wizard dialog did not pre-select "Save in input folder" when that option was the most recently used one.
Fixed an issue that could arise when migrating a workflow containing Create Sequencing QC Report where the workflow was originally created using the CLC Genomics Workbench 6.5 or older.
Fixed an issue that made "Download and save" fail when invoked on a Blast editor.
Updated the URL to use for links to UniProt databases.
Various minor bug fixes.

New in CLC Genomics Workbench 9.0.1 (Jun 11, 2016)

New in CLC Genomics Workbench 9.0 (Mar 31, 2016)

NEW FEATURES AND IMPROVEMENTS:
New tools:
Import Metadata - basic and easy metadata import. This tool supplements the tools available in the Metadata Table Editor.
IMPROVEMENTS:
Workflow related:
Workflow inputs can now be ordered via the Workflow Editor, affecting the order that input information is requested when setting up a Workflow run.
Workflows with multiple input elements, where all input elements will be changed per batch, can now launched in batch by right-clicking on the installed workflow name and choosing the option "Run in Batch Mode...".
Tools in a Worfklow that have been renamed will have both the new tool name and the original tool name displayed in the Workflow Configuration Editor.
RNA-seq related:
The RNA-Seq Analysis tool now computes Transcripts Per Million (TPM) values, which appear as an additional column in expression tracks.
Faster analysis of multiple samples in the RNA-Seq Analysis tool due to caching of reference index files.
Performance improvements for Expression Tracks in RNA-Seq.
Expression track table views now have two new buttons for selecting or copying genes/transcripts names.
Expression tracks now contain links to external databases when available.
Transcript level expression tracks now contain the gene name for each transcript.
Mapping related:
Match score can now be specified in the Map Reads to Reference and Map Reads to Contigs tools.
Map Reads to Reference now outputs an empty read mapping and report when nothing mapped, and empty unmapped reads if everything mapped.
Fixed threads being leaked in Map Reads to Reference when caching of indexed reference sequences was used.
Track related:
The tool Create Mapping Graph can now create a coverage graph over the start positions of reads in a read mapping.
Improved error messaging when trying to import malformed fasta files into tracks.
Metadata related:
The use of partial or exact matching schemes can be chosen when associating data with metadata using the Associate Data Automatically option.
It is now possible to change the type of a metadata column, even if it already contains values. Conversion is only possible when all existing values in the given column can be converted to the new data type.
Usability enhancements in the Metadata Table Editor.
General:
Performance optimization for sizing phylogenetic trees by metadata.
The 3D Protein Structure Database has been updated. Please use the Download 3D Protein Structure Database tool to work with the latest version.
The Download Pfam Database tool has been updated to download version 29.
Improvements to the way Ensembl IDs are parsed to links in tables: stable Ensembl IDs are now correctly parsed to links for all Ensembl-supported organisms (Ensembl release 83).
Substantial speed improvements to BAM export.
The options for saving the output from "batch jobs" have been improved. Outputs can now be saved into a specified single folder in addition to the other established save options.
All Excel sheets in a document are now imported and each sheet has a table created for its contents.
The CSV, HTML and Excel table/tabular exporter now use "Inf" and "NaN" values to replace the ambiguous "?".
In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading.
SAM records with CIGAR strings with no aligned residues can now be handled when importing SAM/BAM files.
Same print settings can now be applied for multiple reports in a single export.
GFF Track Import now supports spaces in annotation names
The "Manage Resources" tab has been removed from the the Plugin Manager.
CHANGES:
Workflow related:
The Create Scatter Plot tool is now Workflow enabled.
The Create MA Plot tool is now Workflow enabled.
General:
The naming rules for the outputs of several tools have been changed to align with those applied by most other tools. The tools affected by these changes are: Local Realignment,Low Frequency Variant Detection, Fixed Ploidy Variant Detection, Basic Variant Detection as well as the legacy variant detection tools: Probabilistic Variant Detection and Quality-based Variant Detection.
Export to clc format now truncates very long filenames.
Versions of individual tools are now reported in the history of output objects.
The default view of the expression tracks has been changed: the table view opens first by default, and some columns are hidden, to simplify the view.
For the NGS importers, the paired reads minimum and maximum default interval has been updated to 1 - 1000.
Plots without any data points will now be skipped when rendering reports.
The annotations "Known variation", "Validated by other experiment", "Ancestral allele", and "Phenotype related", created by variant track import are not used and have therefore been removed from variant tracks.
The Detailed Mapping Report statistics table now shows previously missing values for regions with partial coverage. For fully covered regions these values cannot be calculated, and empty strings are replaced with coverage minimum, average and standard deviation. Numeric sorting is retained by inserting NaN values instead of empty strings, where calculations cannot be made.
RPM package installers for Linux are no longer available.
Associate Data Automatically accepts data elements (not folders) as input.
The 'Database Fields' label shown in the 'Show Element Info' view has been renamed to ' Local Attribute Fields'.
The "Metadata Role Override" parameter that was visible when creating Workflows has been removed.
The user can no longer uncheck "export all columns" for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.
Retirements:
The ChIP-Seq Analysis (legacy) tool has been retired.
BUG FIXES:
Fixed a bug when the download buttons on BLAST result table view failed for nucleotide sequences.
Fixed an error when running merge overlapping pairs on extremely short reads.
BED Export: when exporting block list entries (such as connected exons from mRNA tracks), positions were absolute, but are now relative to the 'chromStart' position.
Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
In heat maps it is now possible again to show colors legend to the left and right of the heat map.
Fixed an off-by-one error for read start positions in the 'Find Broken Pair Mates...' output table.
Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
Fixed an issue where an error was reported if the local realignment tool detected an insertion followed by a deletion in the original mapping. Such positions are now ignored.
Fixed an issue where Workflows were not able to remove intermediate data from permission enabled locations unless the top folder was writable.
Fixed a bug that prevented the output from certain tools to be used as input in the "References" channel of the Map Reads to Reference tool when used in workflows.
Fixed an issue where the "Show results"option in the Processes tab would lead to an error if the results dataset was very large.
Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.
Fixed a bug, where the Reference Data Manager fails to open, when the CLC_References folder is located on a resource (e.g. an external disk), which is currently not available (e.g. the disk might be unplugged/disconnected).
Fixed an issue where an error arose when renewing a borrowed network license.
Fixed a bug that led to the creation of an empty folder for each excluded batch unit.
Fixed a bug that led to the inclusion of the number of excluded batch units in the count of the total number of batch units to be processed.
Added missing percentage signs for identities and gaps in Blast text exports.
A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error.
When the InDels and Structural Variants tool is added to the workflow the "P-value Threshold" parameter did not show up in the Select settings wizard step under "Significance of unaligned ends breakpoints". This has been fixed.
Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
Fixed an issue with Open Copy of Workflow so it now works on all workspaces rather than just the first workspace.
Fix an issue that could lead to an error when a job status description changed while a full description was being generated.
Fixed an issue with handling dates when importing metadata from Excel format files using the Metadata Table Editor.
Fixed a bug that was causing missing report text lines.
Fixed an issue where, when the option to "Skip these updates" was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated.
The "Extract and Count" tool in Small RNA analysis now only accepts sequences and sequence lists. Previously, it incorrectly accepted standalone read mappings or small RNA samples as well.
Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
Fixed an issue where sub-jobs were not resumed after pausing and resuming a batch process.
Fixed an issue where the workflow installer creation keyboard shortcut could be used when it should have been disabled.
Fixed a rare issue that could be triggered by switching editor view with a double click.
Fixed an issue that caused the 'Use random codon' parameter in the tool "Reverse Translate" to report a null-error.
PLUGIN UPDATES AND FIXES:
All plugins need to be installed in the new Workbench for compatibility reasons.
Changes to freely available plugins:
Ingenuity Pathway Analysis: Expanded with a new tool supporting Statistical Comparisons and a Ready-to-Use Workflow for statistical analysis, visualization, and upload to IPA.
Annotate with GFF: Now supports spaces in annotation names.
Batch rename: Fixed an issue where a warning was displayed for entries not modified.
COMPATIBILITY:
This release can be used with CLC Genomics Server 8.0.

New in CLC Genomics Workbench 8.5.1 (Oct 18, 2015)

Bug fixes:
Fixed a bug when the "Search for sequences at NCBI" tool would fail to download nucleotide sequences with the error message "The following sequences were not downloaded correctly: ...".
Fixed a problem with the BLAST at NCBI step of the Create Protein Report tool.
Fixed an issue leading to an error during VCF export where the data involved had originally been imported from VCF files and the values in the QUAL field were integers.
Export of floating-point (decimal) numbers to VCF format were previously dependent on the specified locale. This has been fixed so that the decimal separator now always is a point.
When doing automatic association of metadata, the log now shows which metadata rows were not associated with any data.
Fixed a bug that prevented metadata manual information to be accessed from within the Workbench.
Fixed a bug where doing automatic association using a metadata table stored on a CLC Server would fail.
Automatic association of metadata now handles association based on the a prefix of data names rather and exact matching to the whole data name.
A metadata table no longer needs a key column for its rows to be manually associated with data elements.
An option to override metadata roles previously visible in the configuration of Workflow outputs was removed.
Fixed an error happening when a Workbench Data Location was pointing at a file on the system instead of a folder. It will now appear as unavailable in the Workbench Navigation area.
Enabled tooltips for all parameters when configuring and executing workflows.
The login process from a Workbench to a CLC Server must now complete before opening a clc url will begin.
Fix a problem on Macs where the Workbench was not recognized as a custom protocol handler for clc:// urls.
Resolved a rare occurring exception that could be triggered by switching editor view with a double click.
Fixed a problem where after import of a large volume of data, using the "Show results" option in the process tab resulted in an error.
Changes:
In the output from the Trio Analysis tool, the inheritance option "Accumulative" has been renamed to "Recessive".

New in CLC Genomics Workbench 8.5 (Sep 8, 2015)

New in CLC Genomics Workbench 8.0.3 (Aug 14, 2015)

Bug fixes:
Fixed a read mapper bug that caused some reads to be incorrectly reported as unmapped when global alignment was selected.  
Fixed an issue with the sort order for paired reads in SAM/BAM exports in high coverage regions.
Fixed a SOLiD NGS importer bug where import of very low quality, colorspace encoded paired-end sequence reads in fastq format could lead to paired sequence lists where the wrong reads area marked as pairs.
Fixed an issue where the Local Realignment tool when run with RNA-seq mapping could occasionally report a match that did not meet internal requirements as a valid match. This had a downstream effect when variant calling tools were run, and then failed upon encountering such a position. This issue has also been addressed in this release. 
Fixed an issue where the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools would stop with an error when encountering a place in a read mapping containing a match that did not meet internal requirements of a valid match. 
Selecting an entry in a Blast results table could highlight the wrong alignment in the Blast editor, if the table had been filtered or sorted.
Fixed an issue where an error would arise when using the Design Primers editor and clicking on an annotation on the sequence.
Fixed a bug that caused the mapper to enter an infinite loop if a reference of length 0 was used.
Fixed a rare bug that sometimes made the read mapper halt prematurely when several seeds were identified at the same reference position.
Fixed a rare issue where the Workbench would display an error message when installing a 3rd party licensed plugin.
Fixed an issue where an error would arise in some view types when an region of a sequence had been selected and then the "Zoom to selection" tool was used.
Improvements:
The Illumina import now shows the file name on top of the process bar during the import.
In the "SAM/BAM Mapping Files" import tool, any inconsistencies between the reference sequences in the BAM file and the reference sequences in the CLC software that are provided for the import of the BAM file are now highlighted in red in the "References in files" table.

New in CLC Genomics Workbench 8.0.2 (Aug 14, 2015)

Bug fixes:
Fixed an issue with running BLAST at NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
Added a work around to a java issue that occasionally resulted in the Workbench displaying an uninformative error and requiring a restart to continue working.
The InDels and Structural Variants tool can now better detect variants when using target regions near the edge of the regions.
Fixed a rare error in the Create Statistics for Target Regions tool. The error resulted in a failure when a target region only included the very last nucleotide of a chromosome.
The relative read direction filter in the Low Frequency Variant Detection tool is less strict on variants with large coverage.
The variant callers could enter an infinite loop for certain inputs. This fix adds a check that was unfortunately missing in previous fix for this problem.
Fixed bug in which Local Realignment could produce an illegal read mapping. This only happened for RNA-data.
The variant caller will now fail if it encounters an illegal RNA read mapping. If the variant caller fails with such a message, and if it was run on locally realigned data, then we suggest to re-run the local realignment to avoid the error.
The Reverse Translate tool ignored any genetic code specified in the codon frequency tables. All reverse translation would thus default to the standard genetic code.
Fixed wrong display of "Supported format" when exporting elements from either the Folder Editor or the Local Search Editor.
Fix of potential wrong file being saved when editing a file found via the Local Search Editor.
Plots inside reports are now shown with their saved side panel settings.
Fixed saving different line colors in plots through the side panel.
Side panel option to show legends for a plot with more than 10 samples is now enabled.
Fixed an issue that led to an error when rendering plots for empty data sets.
Fixed text inside variant boxes in the track view sometimes having a small font size.
When installing a workflow with bundled data, it is no longer possible to select a read-only folder for storing the data.
Transcriptomics experiment and sample tables can now be sorted, even with large numbers of rows.
Fixed an issue where the "Empty Recycle Bin” option was sometimes incorrectly unavailable.
A fix was applied to avoid an exception in circumstances when the cleanup of downloaded files from BLAST failed.

New in CLC Genomics Workbench 8.0.1 (Apr 17, 2015)

New features and improvements:
Former plugin "Duplicate Mapped Reads Removal" is now integrated under the name "Remove Duplicate Mapped Reads " and can be found in the NGS Core toolbox. For users that had previously installed this plugin, it needs to be uninstalled.
Link Variants to 3D Protein Structure now generates full biomolecules: even if the PDB template only contains a single subunit, the full multimer can be generated from symmetry information. This makes it possible to locate variants on the interface between protein chains.
The filtering option in the Create Track from Experiment tool only considered the predicted fold-changes in the positive direction, so features that were reduced in expression were filtered out. This has now been fixed.
Transcriptomics experiment and sample tables can now be sorted, even with large numbers of rows.
Particular annotation types (columns) can now be specified for export in Excel, HTML and tab delimited formats.
Added column to output of "Annotate and Merge Counts" indicating 3' or 5' direction when using "grouping on mature" parameter.
Increased the performance for gzip export.
Bug fixes:
Fixed an error that in rare cases would result in a division by zero error message when selecting rows in the Annotation Table view.
Fixed an error that made it impossible to add an annotation via the Annotation Table view if the table is empty.
Fixed rare problem where a track list of reads tracks and graph tracks would break.
Fixed an error affecting the "Cut Sequence Before/After Selection" tool in the Cloning editor.
Fixed bug where a left-click quickly followed by right-click was interpreted as double-click on OS X (in the persistence search result list, in the toolbox tree, and in the workflow editor).
Fixed an error that occurred when running the Create Sequencing QC Report tool and requesting quality analysis reporting..
Fixed an error that prevented the import of adapters from csv format.
Fixed the SOLiD NGS importer to correctly import basespace encoded sequences in fastq files. It is still assumed that sequences originate from colorspace.
It is now possible to filter tables based on content in the 'Link Variants to 3D Protein Structure' column.
Fixed a rare error that caused the Amino Acid Change tool to crash if a CDS feature was less than 3 bases long.
Fixes and updates for automated genome downloads (Zea mays, C. elegans).

New in CLC Genomics Workbench 8.0 (Feb 24, 2015)

New features and improvements:
New tools:
Create Track from Experiment. This tool makes it possible to convert Experiments to Tracks. In the Experiment, the results of the statistical analysis are annotated on the experiment as additional columns. It can be advantageous to visualize the results of the statistical analysis as tracks.
Link Variants to 3D Protein Structure makes it possible to visualize amino acid changes on 3D protein structures. After running the tool on a variant table, variants can be visualized on 3D structures. 3D models are automatically built using structural templates from the PDB. The new tool can be found under 'Resequencing Analysis | Functional Consequences | Link Variants to 3D Protein Structure'.
The Map Reads to Reference tool now supports both linear gap cost parameters and affine gap cost parameters. The addition of affine gap cost support allows you to get more accurate results for reads with stretches of insertions or deletions.
The read mapper used in the RNA-Seq Analysis tool has been upgraded to use the new read mapper described above. This upgrade enables you to run RNA-seq Analysis with as little as 6 GB RAM and at the same time improves your end results. However, you cannot yet use affine gap cost parameters in your RNA-Seq analysis.
Performance of the Merge Read Mappings tool has been improved, especially in situations where the number of reference sequences is very large, such as when merging reads mapped against de novo assembly results.
The tool Amino Acid Changes has been expanded with an extra output that makes it possible to visualize amino acid changes in track format. The amino acid color schemes can be changed in the Side Panel under "Track layout" and "Amino acids track".
Chromosome bands/cytogenetic ideograms can now be downloaded to the Workbench via the Download function. The ideogram can be added to track lists to get a better overview of the data. 
Tracks:
Improved resource management: Makes it more efficient to work with tracks involving large numbers of reference sequences. This typically applies to situations where a reference genome is not available, such as when tracks are based on de-novo assembly results.
Consistent output when enriching variant tracks and annotation tracks with extra table columns. Output tracks from these tools now have the same number of added table columns and the columns will always be in the same order. Previously, if an added column had empty values for all variant rows, it would have been removed from the final table, resulting in varying number and relative order of additional columns when multiple samples were processed with the same tools/workflows. All columns are retained now, facilitating downstream processing of exported tables, and providing immediate visual reference as to which enrichment/annotation tools have been applied, even if they did not produce any results for a particular sample.
Tables for variant tracks and annotation tracks can now sort and filter columns with cells containing multiple numbers.
Improved the track viewer for variant tracks to show the sequence alteration on the rendered variant.
Improved performance of creating variant tracks and annotation tracks.
Graph tracks now show negative values filled upwards to y=0 (as expected). 
Workflows:
When installing a workflow in the workflow manager, the newly installed workflow is automatically selected.
The "Run" button in the workflow editor does not require a saved workflow anymore to be enabled.
In the execution wizard of a workflow the "Reset to default" button is now active.
All icons in the workflow editor are now on the left side.
Introduction of snippets: Parts of workflows can now be saved as a snippet and reused in other workflows.
Installed workflows: It is now possible to create a copy of an installed workflow and open the copy in the view area by clicking once and then right-clicking on the installed workflow in the toolbox. This brings up the option "Open Copy of Workflow". 
MA plots, scatter plots and histograms can now accept expression tracks as input.
An extra optional output called "Create coverage graph", that shows the coverage in each position of the targets, has been added to the tool Create Statistics for Target Regions.
Increased decimals for numbers when exporting table to CSV, tab delimited text, and Excel.
Improved reporting of errors related to low disk space.
New features for the 3D molecule viewer:
Align to Existing Sequence makes it possible to connect a 3D protein chain to a sequence, sequence list, or an existing alignment
Transfer Annotations makes it possible to create atom groups from sequence annotations (and vice versa) for connected sequences.
Improved layout of the property viewer.
Improved PDB import of water molecules, DNA/RNA, and saccharides.
When importing PDB files, the resulting Molecule Project now contains citation information (PDB ID and primary reference), which can be found in the 'Show History' view.
Batching: Processes tab and analysis execution logs now display batch names in addition to analysis names for enhanced clarity.
The External Application Client Plugin is now available directly from the Workbench Plugin Manager.
Bug fixes:
Fixed an error resulting in billions of reads being silently dropped when producing large read mappings against large counts of reference sequences. The error involves a read count overflow and the dropping of at least 2 billion reads per failure instance.
Fixed display problem in read mappings showing too many hidden insertions (as vertical black lines) in certain overlapping paired reads.
Fixed problem with links and text in tables that were being cut off when succeeding a link.
Restriction site analysis: The values "Cut position(s)" column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.
The tool Identify Graph Threshold Areas can now use negative values to define its threshold.
Workflows:
In the workflow editor the "Reset to default" now always reverts to the right names.
In the workflow editor the validation is now correctly triggered when changing the configuration of an input element.
The workflow editor can now open workflows in which the graphical view of the workflow is corrupt.
Fixed an exception which could occur during workflow migration.
Data with the same name can now be bundled multiple times in a workflow installer.
Previously when a plugin contained custom actions and a workflow, the workflow could not be installed. This has been fixed.
Fixed problem with unlocked output names that previously could not be configured during execution of a workflow.
A workflow with configured data from a server is now automatically validated when connected to the server (when opened in the editor). Previously the workflow had to be closed and reopened first.
The original workflow file included in a workflow installer can now be exported directly without having to restart the workbench in advance.”
A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings.
Fixed an error that could cause batch processing to open all results rather than saving them.
Fixed problem with import of BED files using external applications.
SAM/BAM import will no longer fail for alignments with POS = 0, but instead import them as though they were unmapped.
Fixed problem going back in the wizard for the "Find Binding Site and Create Fragments" tool.
Fixed error occurring when removing an unsaved reads track from a track list.
Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.
Fixed error when showing protein translations of annotations shorter than 3 bases.
Search for PDB Structures at NCBI has been fixed to correctly show PDB deposit date and organism type.
Fixed a bug in the Mapping Coverage exporter.
Fixed reads tracks reads-amount indicators (the numbers between the reads track and the box with the tracks name and number of reads) that sometimes wrongly said 0.
Small RNA Analysis -> Annotate and Merge Counts: When you choose to create a “grouped on mature” output, the small RNAs are grouped by both the 5’ and the 3’ mature sequences separately in the “grouped on mature” output. The column heading has therefore been changed to show "Mature" instead of "Mature 5' ".
When using the RNA-Seq Analysis tool with the "One reference sequence per transcript" option, the "Maximum number of hits for a read" option was sometimes not taken into account for multi-hit reads. This has been fixed.
Two problems with the F1 help has been fixed; 1) When pressing F1 in a workflow tool wizard more than one help window appeared, and 2) Fixed problems showing help by pressing the F1 key in tool wizards.
Fixed a bug that in some cases caused an error when annotating read sequence lists with the GFF/GTF/GVF annotation tool.
Amino Acid Change tool: In cases where an mRNA track does not overlap all annotations in the CDS track, "Coding Region Changes" were not added to variants overlapping a CDS but not overlapping an mRNA annotation. This has been fixed.
Variant callers and the "Amino Acid Changes" tool: In cases where variants overlapping an mRNA annotation but not a CDS annotation,"Coding Region Changes" were not added to variants overlapping an mRNA annotation but not a CDS annotation. This has been fixed.
Fixed an error that in rare cases would prevent creation of tracks from references sequences.
Hypergeometric test on annotations: Fixed a rare error that occurred for some data sets containing annotations of the form: '1234 // abc'.
Fixed a bug in the QC report creation step of the ChIP-seq analysis.
Fixed a bug for color space reads in RNA-Seq Analysis that caused all exon-exon matches to be filtered away.
An issue where an XSQ file containing both base space and color space versions of the same reads were incorrectly imported into the same sequence list, resulting in each read appearing twice has been addressed.
The alignment editor view and alignment primer design view now have independent settings.
Changes:
Contigs coming from the de novo assembler will now have underscores in their names rather than spaces.
Plugin updates and bug fixes:
The TRANSFAC Plugin has been updated and now has two modes of operation: "Classic" and "Genomic". The Classic mode is the legacy mode taking sequences as input and annotating these sequences. The new Genomic mode takes regions on a genome (an annotations track) as input. In both modes it is now possible to specify global thresholds of similarity score which can be used to filter the annotations included in the output.
A bug has been fixed with import of metadata containing column names with colons in the Metadata Import plugin.
Compatibility:
This release can be used with CLC Genomics Server 7.0
This release is using the read mapping and de novo assembler that corresponds to CLC Assembly Cell 4.3.

New in CLC Genomics Workbench 7.5.2 (Feb 18, 2015)

Bug fixes:
Fixed an error resulting in billions of reads being silently dropped when producing large read mappings against large counts of reference sequences. The error involves a read count overflow and the dropping of at least 2 billion reads per failure instance.
Fixed error when removing an unsaved reads track from a track list.
Fixed display problem showing too many hidden insertions in certain overlapping paired reads.
Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.
Fixed a bug in the Mapping Coverage exporter.
Fixed reads tracks reads-amount indicators (the numbers between the reads track and the box with the tracks name and number of reads) that sometimes wrongly said 0.
Small RNA Analysis -> Annotate and Merge Counts: When you choose to create a “grouped on mature” output, the small RNAs are grouped by both the 5’ and the 3’ mature sequences separately in the “grouped on mature” output. The column heading has therefore been changed to show "Mature" instead of "Mature 5'".
Two problems with the F1 help has been fixed; 1) When pressing F1 in a workflow tool wizard more than one help window appeared, and 2) Fixed problems showing help by pressing the F1 key in tool wizards.
Amino Acid Change tool: In cases where an mRNA track does not overlap all annotations in the CDS track, "Coding Region Changes" were not added to variants that overlap a CDS but not an mRNA annotation. This has been fixed.
The Low Frequency Variant caller could end up in an infinite loop in certain corner cases. This is now fixed.
Fixed "Export Graphics" default save-as directory.
Fixed problem with import of BED files using external applications.
Hypergeometric test on annotations: Fixed a rare error that occurred for some datasets containing annotations of the form: '1234 // abc'.
Fixed a bug in the QC report creation step of the ChIP-seq analysis.
Fixed error when showing protein translations of annotations shorter than 3 bases.
Fixed a bug for color space reads in RNA-Seq Analysis that caused all exon-exon matches to be filtered away.
Fixed problem going back in the wizard for the "Find Binding Site and Create Fragments" tool.
Fixed a bug that in some cases caused an error when annotating read sequence lists with the GFF/GTF/GVF annotation tool.

New in CLC Genomics Workbench 7.5.1 (Nov 11, 2014)

New features and improvements:
"Filter Annotations on Name" can now insert names to filter on from significantly bigger files. Previously the limit for the file size was 10KB, this has now been increased to 20MB.
RNA-Seq Analysis: The ENSEMBL gene id of each gene, where available, has been added as an additional column to the gene expression track output.
Improved performances of the ChIP-seq Analysis tool for genomes with a large number of chromosomes.
It is now possible to run a workflow without an optional input.
Bug fixes:
A bug has been fixed in the Set Up Experiment tool. Exon-related expression values can now only be selected when present in the individual samples.
When creating a subset of a paired experiment, the sub-experiment no longer appeared as being paired. This bug has been fixed and sub-experiments created in previous versions should recover the pairing information when accessed with this version of the workbench.
Pfam filtering bug fixed. Previously, Pfam only reported the first domain of each type in a query and as a consequence many domains were missed. We recommend that users whose research depends on Pfam annotations re-run the tool on their data.
The AAC tool did not annotate variants in 3' UTR with their DNA-level change using the HGVS c.xxx format. This affects any analysis done with Gx 7.5 or earlier based on ENSEMBL CDS tracks from older versons. The AAC analysis should be redone using Gx 7.5.1 for correct annotation. Important: Please also check the description in the Gx 7.5 release notes of a bug fix in the translation of CDS annotations to protein sequences that was wrong in cases where the reading frame was not +1 or -1 in CDS annotations imported from ENSEMBL.
Fixed problem importing VCF files using the AO and RO genotype field.
Fixed problem importing certain VCF files.
Fixed a bug in the 'Maximum Likelihood Phylogeny' tool that failed when generating bootstrap values for certain input alignments.
Fixed problem with scrolling to the relevant files when selecting objects as parameters in tool wizards.
The Blast text results have been improved so they show the correct query and subject positions regardless of strand.
Fixed a problem that prevented BLAST operations when choosing to run these on the CLC Server.
Fixed problem with import of read mappings with supplementary alignments. When importing read mappings with supplementary alignments, supplementary alignments are not imported. Previously import of such read mappings caused import errors.
Fixed rare problem with coverage that could occur in zoomed out reads tracks containing wrapped paired reads.
Fixed rare error when sorting experiment tables.
Fixed a bug in the Annotate and Merge Counts tool that in rare cases resulted in incorrect sorting and crash.

New in CLC Genomics Workbench 7.5 (Jun 27, 2014)

New features and improvements:
New tools:
New variant callers (Resequencing analysis):
Three new tools for detecting variants are available in the "Variant Detectors" toolbox under "Resequencing Analysis": Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection. Basic Variant Detection and Fixed Ploidy Variant Detection are complete reimplementations of the Quality-based and Probabilistic Variant Detection tools, with improved options for filtering. The Low Frequency Variant Detection tool is a new statistically based tool for detecting low frequency variants e.g. in mixed tissue cancer or mixed population samples. The Quality-based and Probabilistic Variant Detection tools have been moved to the "Legacy tools" folder in the toolbox, and will eventually be retired. 
New read mapper and a tool for downsampling (NGS Core Tools):
New memory-efficient read mapper enables working with human genomes on a modern notebook. Caching of reference index files improves the speed when the same reference is used repeatedly for read mapping. The new memory efficient read mapper replaces the old "Map Reads to Reference" and the name remains the same.
The new "Sample Reads" tool can be used to downsample large sets of reads for all types of NGS analysis.
New ChIP-Seq tools (Epigenomics Analysis):
The ChIP-Seq Analysis tool found in the toolbox under "Epigenomics Analysis" has been replaced with the plugin "Peak Shape ChIP-Seq Analysis" (that has been renamed to "ChIP-Seq Analysis"). The old "ChIP-Seq Analysis" tool has been renamed to "ChIP-Seq Analysis (legacy)" and moved to the new "Legacy tools" folder in the toolbox. The new ChIP-Seq Analysis tool uses a new approach to identify genomic regions with significantly enriched read coverage and a read distribution with a characteristic shape. The parametrization of the algorithm is done automatically by learning the characteristic shape of the signal from the data, making the algorithm intuitive and easily understandable.
The "Annotate with Nearby Gene Information" tool can be used to annotate ChIP-seq peaks with the nearest gene upstream and downstream, based on the start position of the gene. The resulting annotations are provided in the same format as in the legacy ChIP-seq Analysis. 
A new folder called “Legacy tools” has been added to the toolbox. The "ChIP-Seq Analysis (legacy)" has been moved to this folder along with the Probabilistic Variant Detection and the Quality Based Variant Detection tools.
Workflows:
The input information is now shown in the preview dialog and also exported to all formats.
It is now possible to edit the workflow input name by right-clicking on the input name in the workflow.
Tools with object parameters now accept multiple inputs. This applies to e.g. Trio Analysis that now can be run in a workflow using child, mother, and father as input in the same workflow.
Workflows as such can have multiple inputs (though this will disable the batch functionality).
Data can now be directly bundled with a workflow installation. This means that reference data can be packed and shared together with a workflow (only recommended for small data).
A workflow input can be pre-configured. If kept unlocked, it can be used to give a default when executing the workflow.
A text field is added to the side panel, where you can search for elements in the workflow. A found element will be centered and highlighted.
A new editor was added for the workflow to concentrate on configuration.
Workflows can be packaged with a plugin and will get installed when the plugin is installed.
Workflows installed on the server now have an overlay icon in the workbench, to make them easily distinguishable workflows installed in the workbench.
The execution of a workflow in the workbench and on the server were unified to have the same behavior regarding logs, intermediate results and output naming.
Locked settings in the workflow wizard are now again hidden per default when executing the workflow, to give a cleaner, simpler look to the configuration. When expanding, one can see all parameters.
New workflow-enabled tools:
Create sequence statistics. 
Protein Analysis, Pfam domain search:
Pfam Domain Search now uses HMMER3 and the latest Pfam database that can be downloaded with the new tool "Download Pfam Database".
Searching multiple sequences is significantly faster.
New filters are available in the improved Pfam Domain Search tool to enable generation of the same results as the online tool.
Local Search enabled from the menu bar now includes filtering on "Path".
“Zoom tools redesign”: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments and read mappings.
The tracks info panels, with track names in the left side of the track, now wraps information instead of showing a scroll bar.
Saving/applying side-panel settings for tables now works for different tables that share some columns.
Graph Tracks can now be exported to Wiggle file; the span option is now supported in the Wiggle import.
"Filter Based on Overlap" and "Annotate with Overlap Information" now accept Expression tracks as input.
SAM/BAM import. It is now possible to choose to ignore unmapped reads when importing SAM/BAM files.
Fisher's Exact Test. Added options for correction of p-value for multiple testing to Fisher's Exact Test, as Bonferroni correction and False Discovery Rate (FDR).
Speedup: newly created expression tracks will display graph faster.
Copy operations can now be stopped.
Output from "Reverse Translate" can now be a Sequence List.
Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.
CLC Workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
Small improvements of the de novo assembler speed.
Bug fixes:
A bug in the Fisher Exact Test tool that in some cases caused incorrect counting has been fixed. The Fisher Exact Test algorithm now checks if a case variant also exists in a control variant, even if they are of different types (e.g. an SNV variant can exists as a part of an MNV variant).
The right-click menu on certain annotations in tracks was not working when viewing a single track. This has been fixed.
Icons in the workflow editor are now scaled consistently when zooming in or out.
Several issues with the validation display in the workflow editor have been fixed.
A bug has been fixed in the workflow configuration wizard. Previously the input was not taken into account when deciding which parameters were enabled.
Fixed problem where the "space" key did not trigger "Find Conflict" in the stand-alone read mapping editor.
Fixed stand-alone read mappings not showing mismatches and insertions in the overflow graph.
Fixed a bug in the de novo assembler and legacy read mapper which could cause a crash due to a collision of temporary file names.
NGS import tools now work when run via CLC Server.
Changes:
To improve the stability of workflows: If a variant caller finds no variants, an empty track is produced, rather than no output.
Due to upgrade to Java 7, Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.
As of June 2014, COSMIC download requires registration. This means that COSMIC is no longer part of the resources that can be downloaded with the Download Genome Data Tool. You can still register at the COSMIC website, download the file to your computer, and use the Import Tracks tool to import the data.
Compatibility:
This release can be used with CLC Genomics Server 6.5.
This release is using the read mapping and de novo assembler that corresponds to CLC Assembly Cell 4.3.

New in CLC Genomics Workbench 7.0.4 (May 14, 2014)

New in CLC Genomics Workbench 7.0.3 (Mar 28, 2014)

New in CLC Genomics Workbench 6.5.2 (Jan 25, 2014)

Bug fixes:
Fixed: Error message when running analysis on experiments (statistical tests, clustering etc.)
Fixed: track lists would sometimes be rendered empty when scrolling tracks with insertions.
Fixed problem of unresponsive dialogs when running analysis with many reference sequences.
Fixed a problem in track lists that caused the view to crash when there is an insertion at the very end of a chromosome.
The folder used by the Workbench for storing log and settings files on Windows 8 has been updated to follow conventions for Windows 8 which is identical to Windows 7. Any existing settings will be copied to the new location automatically.
Fixed various problems related to launching the Workbench through Java Webstart.
Fixed: Opening a search view for searching sequences at NCBI would sometimes fail.
Fixed: The Target Regions Statistics tool did not handle annotations covering the starting point of circular reference sequences properly. If you are using the tool with annotations spanning across the starting point of a circular reference, we recommend re-running the analysis.
In BAM files created by BWA, non-specific reads are now recognized as such during import. Previously, they were treated as unique reads.
Improved stability of Probabilistic variant detection on huge data sets.
Fixed various stability and performance problems of Maximum likelihood phylogeny.
Fixed problem that caused a crash with extract consensus sequence tool with certain parameter configurations and with read mappings with no reads.
Fixed crash of detailed mapping report tool with certain data sets.
Fixed error in importing SOLiD XSQ files.
Fixed an error when importing BAM files, including problems regarding download of reference sequences.
Fixed a read mapper error occurring under special circumstances when excluding regions of a reference when mapping reads .
Fixed a bug in the Assemble Sequences tool causing some data sets to produce inferior contigs.
Compatibility:
This release is based on CLC Assembly Cell 4.2.1
This release can be used with CLC Genomics Server 5.5.X.

New in CLC Genomics Workbench 6.0.4 Build 90127 (May 24, 2013)

New in CLC Genomics Workbench 6.0.3 Build 89418 (May 9, 2013)

New in CLC Genomics Workbench 6.0.2 Build 60220 (Mar 19, 2013)

Improvements:
An update to the de novo assembly algorithm means that it will only include Ns in the contigs when doing scaffolding, or if the reads themselves contain Ns. Previously, ambiguities in the graph behind the assembly resulted in regions of Ns, but these have turned out to be problematic for customers submitting their results to NCBI, so the algorithm is now taking extra care to avoid this.
VCF export: headers mentioning the name and version producing the VCF file, and the identifier of the origin variant track is also encoded as a CLC URL in the header. The installer of the Workbench will per default associate the CLC URL with the Workbench, so that it can directly open the file. Alternatively, the id can be pasted into the search field in the Workbench to retrieve it.
Fragments generated from restriction site analysis can now be opened in batch. When multiple rows in the fragment table are selected, the right-click menu option will now create a sequence list with all the selected fragments.
For alignments, mappings, BLAST results and other sequence views, the right-click options to Open Copy of Sequence and Open This Sequence have been merged to Open Sequence. If a copy should be created, use Save As with the new sequence, or drag it into a folder in the Navigation Area.
Bugs:
Import or download of UCSC variant tracks was only done partially with no warning to the user. Only variants on chr1 were annotated. This has now been fixed, but we strongly recommend all users downloading or importing variant data from UCSC using Genomics Workbench 6.0 to re-run the import/download using the new version.
Trio analysis tool did not report a reference allele as a de novo mutation, even if both mother and father only had variant alleles at this position. This has now been fixed so that reference alleles are not considered special when analyzing the inheritance.
The RNA-Seq Analysis produced only single reads in the unmapped reads list. This has now been fixed, and we encourage customers using paired reads as input and performing downstream analysis of the unmapped reads to rerun the RNA-Seq Analysis.
In the GO Enrichment Analysis tool for variant data, some columns were missing. This has now been fixed.
When trimming paired data, section 4 in the report did not show the right number of reads used as input.
Several errors related to workflow configuration and execution have been fixed.
Errors related to managing Workspaces have been fixed.
An error occurring when using variant tracks from old versions in the Compare Variants tool has been fixed.
Annotations were added by the Find Open Reading Frames tool, even though the option to add annotations was not selected. This is now fixed.
Fixed an out-of-memory problem in the Create Alignment tool.
The result of the Target Regions Statistics tool is now named after the input file.

New in CLC Genomics Workbench 6.0.1 Build 60110 (Jan 23, 2013)

New in CLC Genomics Workbench 5.1 Build 51003 (Apr 11, 2012)

New in CLC Genomics Workbench 5.0.1 (Mar 15, 2012)

New in CLC Genomics Workbench 4.7.1 (Jun 28, 2011)

New in CLC Genomics Workbench 4.7 (Jun 22, 2011)

New and improved features:
Mapping
Packed view of mapping data: a great improvement of the default way of visualizing NGS reads when mapped to a reference.
New mapping data format supports multiple alignments and allows for import and full visualization of Complete Genomics evidence files in SAM format
New plug-in for gapped read mapping of e.g. cDNA to genomes
New plugin to detect Structural variation
Action to detect structural genomic variation from paired read information
Action to detect copy-number variation (CNV) from coverage information
New and more flexible data structures to recommended nomenclature more closely w.r.t. changes that affect start codons and changes that cause indels at the amino acid level.
Performance of Excel 2010 exporter improved in terms of speed and memory requirements
When using a license server, the Workbench user can now specify a custom user name which can be checked in the license server configuration. This makes it possible to get more fine-grained control of the users of the license server.
Export of trace data in scf format.
BLAST
BLAST parameters have been changed so that number of threads is 1 per default (there is a bug in the BLAST code provided by NCBI which makes it fails on certain data sets when using multiple threads)
The "Mask lower case" option has been removed
Tool to download BLAST databases from NCBI within the Workbench
The BLAST Database Manager has been improved to show when referred databases are missing
Bug fixes:
Fixed: References between SNP tables and mapping results were broken when exporting-importing data.
Fixed: Summary mapping report did not mention customized mapping parameters when running in batch mode
Fixed: Various SAM/BAM import and export errors
Fixed: When running adapter trimming searching on both strands, some reads were marked as "reversed" in the result. The only consequence is incorrect reporting of the number of forward and reverse reads in the mapping results.
Fixed: Mapping report did not calculate read length for individual reads when using paired data
Fixed: Alignment-based primer design failed for columns with many gaps
Fixed: "Find Binding Sites and Create Fragments" did not find binding sites where the primer extended the 5' end of the template sequence
Fixed: DIP detection would crash on large data sets
Fixed: Import of certain special Genbank files failed
Fixed: RNA-Seq report with paired data: total number of reads was counted as pairs rather than individual reads
Changed: RNA-seq transcript variants are named using '.' rather than '_'. Note that it is not possible to create transcript-level experiments based on old and new samples
Changed: Label of Illumina quality score selector has been changed to reflect the 1.8 update of the Illumina pipeline which now uses quality scores on the Phred scale
Various minor bug fixes

New in CLC Genomics Workbench 4.6.1 (Apr 6, 2011)

New in CLC Genomics Workbench 4.0.2 (Oct 21, 2010)

New in CLC Genomics Workbench 3.7 (Dec 15, 2009)

Global alignment for long reads when running reference assembly algorithm
Gapped color-space alignment when running reference assembly
Significantly improved speed of all operations with large data sets
RNA-Seq analysis:
Performance optimization: A run of 44 mio reads against the mouse genome now takes 32 minutes on an eight-core computer with 32GB RAM. This used to be more than two hours. With the previous version, a lot of small temporary files were created and deleted, and this took a long time and impacted the comupter's general responsiveness. In comparison, only a small fraction of temporary files are created with the new version.
New option to specify minimum required exon-overlap of reads spanning an exon-exon junction. Read more...
New RNA-Seq report which gives statistical overview of the assembly process. Read more...
Result table now reports number of exon-exon- and intron-exon junction spanning reads.
Result table now reports chromosome location of genes. Read more...
Visualization of reads that span exon-exon junctions. Read more...
Reads mapping equally well to intron-exon and exon-exon boundaries are now identified as unique exon-exon spanning reads.
RPKM is better defined in the user manual. Read more...
Default setting for multi-hits is now 10 as in the Mortazavi paper Read more...
Very short reads are now assembled allowing more mismatches.
Expression analysis:
Volcano plots: you can now choose the values to plot on the x-axis. Choose between "Difference" and "Fold change". Read more...
Table view of bar plots shows the same intervals as are shown in the bar plot.
Generic importer for expression array data in tabular format. Read more...
Generic importer for expression experiment annotation data in tabular format. Read more...
Gene Ontology (GO) files can now be used to annotate an expression experiment. Read more...
Tag profiling: You are no longer allowed to annotate tag samples, only experiments
Side panel of experiment table has been re-organized to provide better overview. Read more...
Import high-throughput sequencing data:
Import tool moved from Toolbox to File menu and tool bar. Read more..
Import and export of the SAM alignment format. Read more...
Import of alignment data in tab-delimited format, including the ELAND alignment format. Read more...
Import of Illumina QSEQ file format. Read more...
Linker in 454 data is also found for non-perfect matches Read more...
Enhanced visualization of contigs:
Un-aligned nucleotides on the inside of paired-end reads are now shown
Paired-end reads have a single line connecting the pair rather than gaps
Drag handles to move the aligned/unaligned border are only shown when you can see the bases of the reads. This means that you need to have zoomed in to 100% or more and chosen Compactness levels "Not compact" or "Low". Otherwise the handles for dragging are not available (this is done in order to make the visual overview more simple). Read more....
It is possible to display pairs that overlap
The unassembled reads from an assembly now preserves their paired-end status (this also means that you can get two lists - one with pairs and one with the remainder of the broken pairs
SNP detection output table now reports if multiple non-synonymous SNPs exist in same codon
SNP detection dialog: Quality filtering is no longer disabled when quality scores are missing. Due to performance issues it is not possible to check if quality scores are present. The SNP detection will just omit the quality score filtering if quality scores are not present.
SNP detection: possible to detect variants with frequency less than 1 percent.
Contig report now includes information about coverage for both covered regions and whole reference. Read more...
Opening consensus sequence including gaps will also put Ns before the consensus sequence starts and after it ends
The trim functionality now includes the option to trim away a predefined number of nucleotides from either end of a read. Read more...
Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones. Read more...
Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments. Read more...
In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu. Read more...
Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments. Read more...
Deployment:
You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more...
Support for removing tools accessing the internet (NCBI BLAST, update notifications etc). Read more...
General import and export:
Support for import of complex regions from GFF files
Export tables and reports in Excel format.
Import section of user manual re-structured to provide better overview Read more.... Expression data importers are now described in technical details in a separate section Read more....
You can now export multiple sequence lists in fasta format
Forced import of zip files is now supported (it will force import the contents of the zip file)
The standard import now accepts gzip and tar files as well as zip
If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files
Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: "product", "locus_tag", "protein_id" and "transcript_id"
When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.
When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales)
GFF plug-in has been updated to accept complex annotations
Miscellaneous:
Advanced retyping of annotations using the annotation table. Read more...
Improved reporting of situations when a full disk prevents saving of data
Downloading sequences using drag and drop from the search table no longer creates a "Downloading..." node in the folder. The download process can be monitored in the Processes tab.
Primer design now supports PCR fragments longer than 5000 bp.
Extract Sequences moved from File manu to Toolbox-> General Sequence Analysis. Read more...
Better progress feedback on various dialogs
Bug-fixes:
Problem with order of genes when setting up RNA-Seq experiments. If the order of input sequences was not the same for all samples, the experiment would be wrong.
Fixed wrong orientation of SOLiD mate-pair data
Fixed problem with naming of tabs. The fix means that on Windows and Linux unsaved data now gets a * rather than make the tab name bold and italics. (This has always been the behavior on Mac OS X).
Fixed problem displaying the "Copying..." label when copying data and then updating the folder
Misleading label when assembling reads shorter than 15 bp. Now it says that these reads will be ignored in assembly

New in CLC Genomics Workbench 3.6.5 (Oct 8, 2009)

New in CLC Genomics Workbench 3.5.1 (Jun 12, 2009)

New in CLC Genomics Workbench 3.5.0 (Jun 2, 2009)

Data formats: Data generated with version 3.5 cannot be read in earlier versions.
New features:
New ChIP seq tool.
Contig report that records various statistics and graphs for contigs, including e.g. N75, N50 and N25 statistics, coverage distribution, contig size distributions.
Extension of RNA-seq functionality to also handle color space data
RNA-seq now outputs and can use unique and total gene/exon reads as well as median coverage as measures of expression.
Implementations of statistical tests for comparing expression levels of count-based expression measures as may be produced in RNA-seq
Kal's test for differences of proportions in single sample to single sample comparisons.
Baggerley's test for differences of proportions in two groups with replicates comparisons.
New filter options in SNP and DIP detection.
SNP and DIP detection: as supplement to minimum variant frequency in percent, you can also specify a minimum variant count.
SNP detection: just as DIP detection there is a maximum coverage filter.
SNP detection: there is now a "ploidy" setting just as for DIPs. This is used to mark SNPs as "complex". The "Genetic code" drop-down box has been moved to step 3.
Alignment of SNP and DIP tabular output to allow for easy merging of SNP and DIP tables into complete variance tables.
Support for Sanger Institute defined FASTQ and new Illumina format (QSEQ).
Import of NGS data now allows discarding of sequence names for large savings in disc space and processing time.
Performance optimization when adding sequences to a sequence list. This now works for NGS data also.
SNP and DIP detection can now be performed directly on RNA-seq output contig tables.
Exporting coverage graph to csv file now has an option to include or exclude gaps. Excluding gaps will make the file use the reference sequence coordinates.
Much improved memory performance and processing time of large data sets.
Improved performance when handling trace data. Trace now take up 50 % less disk space. This means that the data is opened and saved much faster and less memory is used.
You can now specify minimum length of contigs to be reported in de novo assembly.
"Reverse Contig" has been renamed to "Reverse Complement Contig." Functionality is un-changed.
Import of Illumina expression bead arrays and bead array annotation files.
Import of Affymetrix Chp files (CHP / PSI).
Transformation of expression values now supports square root transformation.
Better feedback on processes: there is a tool tip showing details and start time.
Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
Bug fixes:
Fixed error when trimming reads for vectors.
Fixed out-of-memory error in mRNA sequencing.
Fixed error in mRNA sequencing when gene annotations were present outside the reference sequence.
Fixed error when parsing files from Clone Manager (cm5-files).
UniProt search works again.
Note: This version introduces a new data format which is not readable by older versions of the software.

New in CLC Genomics Workbench 3.2.0 (Mar 12, 2009)

New in CLC Genomics Workbench 3.1.0 (Mar 12, 2009)

New in CLC Genomics Workbench 3.0.1 (Feb 5, 2009)

New in CLC Genomics Workbench 3.0 (Jan 30, 2009)

New features:
Expression analysis including digital gene expression:
Support for both microarray- and sequencing-based (RNA-Seq) expression data
Visualization: Interactive heat map, table and scatter plot views
Transformation and normalization tools
Quality control tools including principal component analysis, MA- and boxplots
Experimental design tools for two- or multiple group comparisons
T-tests and ANOVA analysis with support for paired/repeated measures
Multiple testing corrected p-values (Bonferroni and/or FDR)
Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
Ability to import NetAffx annotation arrays and adding annotation to experiments
Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. 'GO'stats or specific protein pathways).
Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
Facility for annotating sequences from GFF or GTF files (as used by Ensembl and the UCSC Genome Browser), useful for annotating reference genomes before assembly
Statistics on numbers of matching and unique gene, exon and exon-exon boundary spanning reads
Calculation of gene expression measures (RPKM) from mRNA sequence data and generation of gene expression profiles (RNA-Seq analysis)
Discovery of novel transcripts/exons through mapping of mRNA reads to whole chromosomes or genomes, comparing matches with known exons
Interactive views of assemblies and derived gene expression data
Assembly:
Long reads assembly significantly faster
No upper limit on number of reads in de novo assembly (there is still a limit regarding the size of the genome)
New simple output option for de novo assembly: only generate consensus sequence instead of full contigs. At the last step of the de novo assembly wizard, you can now choose between "Full contigs" and "Simple contig sequences". The latter option will result in a sequence list with all the consensus sequences. This is much faster and less the demanding for the computer. You can always create full contigs later by running a reference assembly with the consensus sequences as references.
Quality of trimming for contamination from own sequences improved. It is now possible to trim off smaller primer sequences.
SNP detection:
Accepts multiple contigs and table of contigs (the table output includes a new column for the name of the contig)
For coding regions (annotated with CDS/ORF annotations): changes on the amino acid level as a consequence of a SNP is now reported (both in the table and in the annotations).
General performance improvements
Right-clicking a graph (e.g. coverage) on a contig lets you export the data points to a csv file.
Contig table shows latin and common name of reference sequences. This is beneficial if you perform a reference assembly against references from different species.
Multiplexing - Process Tagged Sequences now has an option to filter away groups with few sequences. This is an advantage if you have very ambiguous barcode definitions where sequencing errors would lead to a lot of "false" groups. These groups can now be filtered because of their small size. (The option is called "Minimum number of sequences" and is found in the third step of the wizard.)
Coverage info is now included when you export a table of contigs in ace format. (It contains a "Contig Tag" of type comment (a CT clause) containing a textual description of the coverage in the form "Average coverage: 14.65". )
Coverage info is put into the description of consensus sequences extracted from a table of contigs (this means that if you export to fasta, this information will be included).
Importing assemblies with more than one contig creates multi contig tables (ace and cas file import)
Improved user experience of processes:
Non-modal feedback from processes:
When there is a message (e.g. from a BLAST search: not hits found)
If you have chosen to save the results in the last step of the wizard, you will be notified when the process is done.
Processes running on the CLC Science Server will notify when they are done.
Possibility to open results by clicking the button next to the process
Possibility to find and select results in the Navigation Area by clicking the button next to the process
You can see a log of your process by clicking the button next to the process (even if you did not choose to see the log in the last step of the wizard)
Support for interacting with CLC Science Server:
Read more at http://www.clcbio.com/index.php?id=1260
3D editor re-design:
The 3D editor now allows you to select individual structure subunits, residues, active sites, disulfide bridges and even atoms, and to customize their appearance
General improvements:
Limited mode: when using a license server - if there are no more licenses left, you can still access your data. The Workbench will then run in Limited mode where only a few tools are available (corresponds to the tools found in CLC Sequence Viewer). Click "Limited Mode" in the license dialog.
Tables:
New advanced filter to use numerical data for filtering and to combined several filter criteria. Click the small button next to the normal filter to see the advanced filter.
Visual feedback when sorting and filtering tables
Improved automatic detection of column width
Performance of graphs and plots improved
Local BLAST is upgraded to use NCBI BLAST version 2.2.19
More elaborate error reports including error logs
You can specify which folder the Workbench should use for temporary files
Extract sequences from a sequence list, contig or alignment by right-clicking the white empty space. You will then be able to extract the sequences into a list or as separate sequences.
The "Find" option in the Side Panel of sequence views automatically detects if you have entered a position instead of a sequence.
Plug-ins:
Extract Annotations plug-in has been improved:
Possibility to specify the naming of the sequences (based on annotation name, type etc)
Performance improvements to make it possible to extract annotations of large genomes.
MLST plug-in: various bug fixes
Bug fixes:
Locale settings were not automatically set right on the first start-up. The locale settings determine whether . or , should be used for before decimals. For new installations of the Workbench, it will now be set to the locale of the computer's operating system. For existing installations, you will have to change this in the Edit->Preferences dialog.
Fixed problem when BLASTing with an empty sequence
Various performance improvements and bug fixes

CLC Genomics Workbench Changelog

What's new in CLC Genomics Workbench 9.5.2

New in CLC Genomics Workbench 9.5.1 (Sep 29, 2016)

New in CLC Genomics Workbench 9.5 (Sep 17, 2016)

New in CLC Genomics Workbench 9.0.1 (Jun 11, 2016)

New in CLC Genomics Workbench 9.0 (Mar 31, 2016)

New in CLC Genomics Workbench 8.5.1 (Oct 18, 2015)

New in CLC Genomics Workbench 8.5 (Sep 8, 2015)

New in CLC Genomics Workbench 8.0.3 (Aug 14, 2015)

New in CLC Genomics Workbench 8.0.2 (Aug 14, 2015)

New in CLC Genomics Workbench 8.0.1 (Apr 17, 2015)

New in CLC Genomics Workbench 8.0 (Feb 24, 2015)

New in CLC Genomics Workbench 7.5.2 (Feb 18, 2015)

New in CLC Genomics Workbench 7.5.1 (Nov 11, 2014)

New in CLC Genomics Workbench 7.5 (Jun 27, 2014)

New in CLC Genomics Workbench 7.0.4 (May 14, 2014)

New in CLC Genomics Workbench 7.0.3 (Mar 28, 2014)

New in CLC Genomics Workbench 6.5.2 (Jan 25, 2014)

New in CLC Genomics Workbench 6.0.4 Build 90127 (May 24, 2013)

New in CLC Genomics Workbench 6.0.3 Build 89418 (May 9, 2013)

New in CLC Genomics Workbench 6.0.2 Build 60220 (Mar 19, 2013)

New in CLC Genomics Workbench 6.0.1 Build 60110 (Jan 23, 2013)

New in CLC Genomics Workbench 5.1 Build 51003 (Apr 11, 2012)

New in CLC Genomics Workbench 5.0.1 (Mar 15, 2012)

New in CLC Genomics Workbench 4.7.1 (Jun 28, 2011)

New in CLC Genomics Workbench 4.7 (Jun 22, 2011)

New in CLC Genomics Workbench 4.6.1 (Apr 6, 2011)

New in CLC Genomics Workbench 4.0.2 (Oct 21, 2010)

New in CLC Genomics Workbench 3.7 (Dec 15, 2009)

New in CLC Genomics Workbench 3.6.5 (Oct 8, 2009)

New in CLC Genomics Workbench 3.5.1 (Jun 12, 2009)

New in CLC Genomics Workbench 3.5.0 (Jun 2, 2009)

New in CLC Genomics Workbench 3.2.0 (Mar 12, 2009)

New in CLC Genomics Workbench 3.1.0 (Mar 12, 2009)

New in CLC Genomics Workbench 3.0.1 (Feb 5, 2009)

New in CLC Genomics Workbench 3.0 (Jan 30, 2009)

New in CLC Genomics Workbench 2.1 (Nov 20, 2008)