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Bandage Changelog

What's new in Bandage 0.9.0

Jan 7, 2022
  • Built to work with Qt 5.15 and Qt 6.2.
  • Runs natively on Apple Silicon Macs.
  • Fixed display issues with dark mode.
  • Added support for SKESA fasta files.
  • Fixed --colour blastrainbow with bandage image (#74).
  • Added version number to the Mac app bundle (#76).
  • Fixed bug with incorrect orphaned node size with bandage info (#90).
  • Added custom as a colour option for command line usages (#96).

New in Bandage 0.8.1 (Dec 20, 2016)

  • Binaries:
  • The Mac app bundle should work on OS X 10.8 and later versions.
  • The Windows executables should work on Windows 7 and later versions.
  • Linux executables were built on two distributions: Ubuntu 14.04 and CentOS 6.7. Try whichever is more closely related to your distribution. They are also available with the Qt GUI libraries dynamically linked and statically linked. The dynamic versions provide a more native GUI experience but require the Qt5 libraries. The static versions do not require the Qt5 libraries and have fewer dependencies.
  • New features:
  • Improved support for Canu
  • Support for Unicycler graphs
  • New layout type: linear layout (appropriate for reference genome graphs and plain FASTA files)
  • New layout option: component separation
  • Improved graph layout component packing
  • Bug fixes:
  • Performance fixes for large BLAST searches
  • Fix crash when BLAST searching for a query with no hits

New in Bandage 0.8.0 (May 4, 2016)

  • New features:
  • Label text dynamically scales with the zoom level, reducing the need to manually change font size.
  • A new command line tool, Bandage reduce, which provides a GUI-free method of saving smaller subsets of larger graphs.
  • A new command line tool, Bandage info, which displays statistics about a graph file. A 'More info' button in the GUI provides the same information.
  • Improved GFA support. GFA files can be loaded which do not directly include their sequences (instead using a *). If they instead keep their sequences in a separate FASTA file of the same name (as is done in ABySS), Bandage will load the sequences from the FASTA when are needed (thanks, Shaun Jackman).
  • Support for ASQG graphs (used by SGA and StriDe)
  • Custom colours and labels are included in saved GFA graphs and will be applied when loaded.
  • When loading a CSV of graph labels, a column named 'Color' or 'Colour' will be used to set custom node colours (thanks, Tyler Barnum).
  • Bug fixes:
  • Fix issue on Mac which could cause a crash when double-clicking the app bundle (but not when launching from the command line).
  • Fix issue where BLAST queries ending in a semicolon didn't work.
  • Better handling of nucleotide BLAST queries that contain N characters.
  • Tolerate node depths of zero or negative depths.
  • Fix overflow bug which could lead to incorrect node lengths.
  • Other changes:
  • The OGDF code for graph layout is now included in the Bandage repository, simplifying the build procedure.
  • Better zoom level limits.
  • Refined command line help formatting.
  • Changed 'Read depth' to 'Depth' in Bandage GUI - more general and hopefully less confusing (thanks, Israel O. Dilán).

New in Bandage 0.7.1 (Dec 11, 2015)

  • New features:
  • Can load plain FASTA files
  • New querypaths command line tool to output BLAST queries without the GUI
  • Bug fixes:
  • Command line functions which do not require the GUI no longer require the X Window System.
  • Removed unnecessary characters from the start of Trinity node names (thanks, Farbod Emami!)
  • Fix code to compile on CentOS
  • Add support for GFA files with missing sequences
  • Fix behaviour when rotating the view via Ctrl-right click dragging over a node
  • Fix path sequence extraction for single circular nodes
  • Fix bug with BLAST hit query coverage filter

New in Bandage 0.7.0 (Dec 11, 2015)

  • Features:
  • Graph editing functionality: delete nodes/edges, duplicate nodes and merge nodes
  • Manually set node names and node read depths
  • Save graphs to GFA files
  • Support SPAdes 3.6.1 assembly graphs
  • Bug fixes:
  • Fixed issue preventing BLAST searches from working in Trinity graphs

New in Bandage 0.6.4 (Dec 11, 2015)

  • Features:
  • Load CSV data to display on graph (thanks, Elmar Pruesse!)
  • BLAST hit filters to refine searches
  • Web BLAST sequences directly from Bandage
  • New graph scope: Read depth range
  • Show mean read depth for selected nodes
  • Two-finger gesture controls for supported trackpads
  • Bug fixes:
  • Fix unit test data directory
  • Change web link to online Bandage help
  • Improve support of data types in scientific notation
  • Fix bug prevent BLAST functionality on Trinity graphs

New in Bandage 0.6.3 (Dec 11, 2015)

  • Features:
  • Individual BLAST queries can be shown/hidden on the graph
  • BLAST query table and BLAST hits table can be sorted by column
  • Now possible to copy from BLAST tables
  • New dialog showing details of BLAST query paths
  • Filtering BLAST query paths
  • Better highlighting of paths on graph
  • Highlighting of BLAST query paths on graph
  • BLAST error messages are more informative
  • Bug fixes:
  • Fix issue with copying text from the GUI
  • Fix GUI tab order
  • Fix BLAST table column sizing

New in Bandage 0.6.2 (Dec 11, 2015)

  • Features:
  • Ability to copy/save paths from the graph
  • BLAST searches find graph paths to match queries
  • Automatically determine node overlap for FASTG files
  • Bug fixes:
  • Fix issue with deletion of temporary directory

New in Bandage 0.6.1 (Dec 11, 2015)

  • Features:
  • tblastn is used to allow for protein queries.
  • Now possible to view all BLAST searches on the graph simultaneously.
  • BLAST queries are assigned colours which can be seen on the graph using the new 'BLAST hits (solid)' colour scheme.
  • BLAST queries can be renamed and individually deleted.
  • Multiple query FASTA files can be loaded at once.
  • BLAST searches now possible from the command line with the --query option.
  • BLAST hits can be labelled on the graph.
  • Bug fixes:
  • Fix issue with node lists when using 'Around nodes' graph scope.
  • Prevent duplicate query names, which could cause problems.

New in Bandage 0.6.0 (Dec 11, 2015)

  • BUG FIXES:
  • Fix issue with rotated labels when saving entire scene to an image file
  • Improve quality of text outlines
  • Expand scene boundary when nodes are dragged outside
  • FEATURES:
  • Allow image saving in vector-based SVG format
  • Preliminary GFA support
  • Simplify graph loading into a single open file dialog
  • Node labels stay in view as the graph is zoomed and panned
  • Additional settings for controlling random node colours
  • Enhanced command line functionality:
  • Most Bandage settings can now be specified using command line options.
  • 'Bandage load' allows users to specify a graph to load and potentially draw on launch.
  • 'Bandage image' allows users to generate an image file without ever opening the Bandage GUI.
  • Change node IDs from integers to strings:
  • This feature is particularly useful for Trinity, where transcript/component names can now be displayed in Bandage.
  • With this feature, partial node searches are now possible, so the user can find/draw nodes with names that partially match a string.

New in Bandage 0.5.6 (Dec 11, 2015)

  • Features:
  • When drawing a graph in double node, nodes and their complement nodes are now shifted slightly apart.
  • Create a new, lower quality setting for graph layout, appropriate for very large graphs.
  • Add website link to 'Help' menu.
  • Bug fixes:
  • Fix rounding issue where the viewport zoom didn't always change when it should.
  • Allow a wider range of node and edge widths.

New in Bandage 0.5.5 (Dec 11, 2015)

  • Features:
  • Bandage now automatically chooses a 'Base pairs per segment' setting when a graph is loaded. Users can switch between this automatic value or a user-specified value.
  • A more flexible system is used for determining node width using coverage. It allows for non-linear relationships, preventing very high coverage nodes from appearing excessively wide. A plot in the settings dialog previews the function between node coverage and node width.
  • Bug fixes:
  • Performance fix for when node width is changed for a large graph.
  • Performance fix for unloading large graphs.

New in Bandage 0.5.4 (Dec 11, 2015)

  • Features:
  • A filename can be passed as a command line argument, and Bandage will load the file immediately upon opening.
  • Bug fixes:
  • Fix bug when BLAST queries end in a dot
  • Fix potential crash when specifying Trinity.fasta node numbers in the 'Around nodes' graph scope
  • Fix misplaced help icon in settings dialog