What's new in FastQC 0.11.3
Mar 26, 2015
- This is a minor bug-fix release which addresses some issues reported with the v0.11.2 release.
- Fixed a bug when using the limits.txt file to disable the per tile analysis module.
- Fixed a documentation error in the duplicated sequences plot.
- Fixed a thread safety bug when processing multiple files in a single session which caused the program not to exit when all processing had in fact completed.
- Fixed a bug which meant that forced formats in the interactive application weren't being honoured.
- Fixed a bug in the way soft clipping was applied when we were analysing only mapped data.
- Fix a memory issue when trying to parse tile names in cases where we mistakenly think we're identify tile numbers, but we aren't
- Fix a bug in the text reporting of per-tile quality scores
- Add the SOLID smallRNA adapter to the default adapter search set
- Fix a bug in casava mode when using uncompressed fastq files
- Increase the number of sampled sequences in the duplicate and overrepresented module to 100,000.
- Add a clean up of data structures for the Kmer module so that the interactive mode can process more files without dying.
New in FastQC 0.11.2 (Mar 26, 2015)
- This is a minor bug-fix release which addresses some issues reported with the v0.11.1 release.
- Added a proper implementation of a --limits command line option to allow users to specify a custom limits file for an individual run. This also fixed a bug seen if the user used the adapter option.
- Fixed an error in the naming of the folder inside the zip file such that it couldn't be extracted into the same folder as the main HTML file.
- Fixed an overly large data structure which was causing some runs to terminate due to a lack of memory.
- Fixed a poor implementation in the Kmer module which was causing unusually high memory usage.
- Fixed incorrect defaults for the warn/fail values in the per sequence quality module.
New in FastQC 0.11.1 (Mar 26, 2015)
- The major new features in this release are:
- Configurable thresholds for modules. For all modules you can now alter a configuration file to set the thresholds used by the program for warnings and errors so that you can flag up only the types of problem which you are concerned by.
- Optional modules. The same configuration file used to set the warn / error thresholds can also be used to selectively disable modules you don't want to see at all.
- New per-tile quality analysis. If you are running Illumina libraries through FastQC it will now analyse the quality calls on a per-tile basis and will flag up points in the run where the quality in individual tiles fell below the average quality for that cycle. This can help to spot technical problems during the run.
- New adapter content module. A new module has been added to specifically search for the presence of adapters in your library. This operates in a similar way to the existing Kmer analysis but allows you to specify individual adapter sequences to screen and will always show the results for each adapter so you can easily
- see what you might gain if you chose to adapter trim your library.
- Improved duplication plot. The duplication plot has been given an overhaul so that it now reports values which are real read numbers rather than always giving relative values. This is thanks to work done by Brian Howard of sciome.com who worked out the right way to extrapolate from the data we sample to the full library. It also shows how the level of duplication would affect the library both before and after deduplication, and the headline figure is now much more useful as it shows the percentage of the library which would remain if you chose to deduplicate.
- Improved Kmer module. The Kmer module has been changed so that instead of trying to search for individual Kmers which are present at higher than expected frequency (which actually happens all the time in real libraries), it now looks for Kmers which are present in significantly different amounts at different starting positions within the library. This has allowed the use of longer Kmer sequences to give a more useful result.
- Since file reports. The default output format for the program is now a single HTML file with all of the various graphs embedded into it. The .zip file output with the individual graphs is still produced as are the associated data files, but you can just distribute the one HTML file alone - the other data is no longer
- required.
- Ability to read from stdin. If you want to pipe a stream of data into fastqc rather than using a real file then you can just use 'stdin' as the filename to process and then stream uncompressed fastq data on stdin.
- Changed base groupings. For long reads we used to use an exponential series to group bases together to summarise the sequence content and qualities. We've now switched the default to be that for grouped plots the first 9 individual bases will always be shown (since this often roots out problems in the libraries), after that there will be a series of evenly sized windows so that the same number of bases fall into each window. You can bring back the old behaviour with the new --expgroup option, and you can remove grouping all together with the --nogroup option (although this will do bad things to your plots if you have really long reads).
- Dropped support for the Solaxa64 (but NOT Phred64) encoding. We have removed the ability of the program to reliably detect the original Solexa64 encoding which was used in the GA pipeline prior to v1.3. This was a 64 offset encoding but which allowed scores which ranged down to -5. Supporting this encoding meant that we would incorrectly guess the encoding on Phred33 files which had no bases with quality scores below 26, which could happen if you aggressively trimmed your data. Supporting just Phred33 and Phred64 now means that we wouldn't mis-detect unless there were no bases with qualities below 31, which is much less likely, even in trimmed data. Since no Solexa64 data will have been produced since early 2009 it is unlikely that removing support for this format will adversely affect users of the program.
New in FastQC 0.10.1 (Feb 12, 2013)
- A work-round has been put into place for a limitation in the java gzip decompressor, where it would read only the first compressed block in a file created by concatenating multiple gzipped files directly, rather than decompressing and recompressing them.
- Users who had installed the program in directories containing characters required to be encoded in URLs (= & ? etc) were finding that the report generation generated an error. This encoding has now been fixed and the program should now have no limits in the name of the directory in which it can be installed.
- One additional feature is that in the fastqc wrapper
New in FastQC 0.8.0 (Jan 22, 2011)
- Made all graphs easier to interpret
- Added an option to analyse only mapped sequences from a BAM/SAM file
- Added an option to analyse two or more files in parallel
New in FastQC 0.7.2 (Jan 14, 2011)
- Fixes a bug in libraries where no unique sequences were observed.
- It also improves the collection of duplicate statistics on libraries with very low diversity.
- A new command line option has been added to allow the user to manually specify a contaminant's file rather than using the sitewide default.
- This would be useful if you have different sets of contaminants to screen against for different libraries, or if you wanted to make a custom set of contaminants, but didn't have sufficient privileges to modify the sitewide contaminants file.