Version History
Version 2.3 - May 19, 2023
qualimap_v2.3.zip
Changes:
- BAM QC: include support in region text report
- Allow 3-column BED file parsing (suggested by Alex Peltzer)
- BAM QC: report secondary alignments and ignore them from main coverage analysis (reported by Sonia Agrawal)
- BAM QC: fix Ns collection from RNA-seq alignment (reported by C. Ruckert)
- BAM QC: fix counts of supplementary alignemnts (reporeted by Alexander Seitz)
- Adjust Qualimap non-zero code return (implemented by Valentin Krasontovitsch)
- BAM QC: fix issue with plotting from OpenJDK (reported by Adrian Garcia Moreno)
- RNA-seq QC: fix error reports for missing chromosomes
- Multi BAM QC: fix OpenJDK issue (reported by Marcel Kucharik and Michal Lichvar)
- BAM QC: fix reverse strand specificity issue (reported by Florian Pflug)
- BAM QC: add coverage std to text report
- RNA-seq QC: add settings control for 5'-3' bias comptuation (suggestion from Ryoji Amamoto)
- BAM QC: allow set maxium coverage size in zoom-in histogram
- BAM QC: add option to control maximum duplication rate in the plot (suggestion from Xiao Lei)
- CountsQC: Added header detection ( implemented by Viktor Horvath)
- BAM QC: add hg38 for GC content inspection
Version 2.2.1 - October 4, 2016
qualimap_v2.2.1.zip
qualimap_v2.2.1_src.zip
Changes:
- BAM QC: fixed issue with paired-end reads only singletons (reported by Anrold Liao)
- BAM QC: adapted novel SAM flag for multiple alignment segments ( reported by Alexis Groppi)
- BAM QC: fixed issue with mapping quality report inside regions (reported by Teresa Requena)
- BAM QC: added support for counting Ns in read alignments
- BAM QC: fixed issue with chromosome limit in coverage plot
- RNA-seq QC: strand-specificity is estimated in case default non-strand-specific protocol stated in the settings
- RNA-seq QC: fixed problem with incorrect BAM records
- RNA-seq QC: number of correctly marked reads without proper pair reported in a single warning
- Allowed names with spaces in provided file/folder path for analysis
- Multi-BAM QC: include strand specificity option for estimation of valid strand reads in each BAM QC report
Version 2.2 - January 29, 2016
qualimap_v2.2.zip
qualimap_v2.2_src.zip
Changes:
- BAM QC: added a novel option to control the skipping of duplicate alignments (reported by Patrik Smeds and Vlad Saveliev ) The default mode was switched to skip marked duplicates only.
- BAM QC: fixed issue with processing alignments (reported by Roberto Spreafico)
- BAM QC: fixed fail when zero mapped reads inside of region (reported by Jochen Singer)
- BAM QC: improved the number of windows output (reported by Alexander Peltzer)
- BAM QC: integrate mm10 support to command line
- BAM QC: fixed insert size histogram computation
- Multisample BAM QC: implmeneted support for per sample groups/conditions
- Multisample BAM QC: added novel statistics report and global coverage plot (suggested by Angela Heck )
- RNA-seq QC: fixed the numbers of reads computation for paired-end reads (reported by Priyanka Jain )
- Documentation: updates in BAM QC, Multisample BAM QC, RNA-seq QC
Version 2.1.3 - October 29, 2015
qualimap_v2.1.3.zip
qualimap_v2.1.3_src.zip
Changes:
- Fixed a problem with removal of provided existing output folder in command line mode (reported by Nathan McNeil)
- BAM QC: added the mm10 GC-content distribution template (suggested by Priyank Shukla )
- BAM QC: fixed issue with report of duplication rate in regions ( thanks to Christian for the report )
- BAM QC: stabilzed default text output number format (reported by Max Koeppel and Henri-Jean Garchon )
- Counts QC: fixed issues with single sample adaption ( reported by Yung-Chih Lai )
- Documentation: update introudction, BAM QC, RNA-seq QC and F.A.Q. blocks
Version 2.1.2 - September 23, 2015
qualimap_v2.1.2.zip
qualimap_v2.1.2_src.zip
Changes:
- BAM QC: added an option to analyze overlapping paired-end read alignments (suggested by Eva Koenig)
- BAM QC: fixed processing of incorrect alignments (reported by Alexander Peltzer)
- BAM QC: improved paired reads statistics description (suggested by Jochen Singer)
- RNA-seq QC: fixed issue with transcript high coverage (reported by Daniel Barrel)
- RNA-seq QC: added to statistcs number of intronic/intergenic reads overlapping exons
- RNA-seq QC: minor fix of coverage plot
- Counts QC: fixed an issue due to update of NOISeq package
- Multisample BAM QC: corrected labels in coverage and GC-content plots (reported by Franziska Singer)
- Multisample BAM QC: fixed issue with min X-value in insert size plots (reported by Roland Schmucki)
- Improved PDF format output
- Documentation: update BAM QC, RNA-seq QC descriptions
Version 2.1.1 - June 15, 2015
qualimap_v2.1.1.zip
qualimap_v2.1.1_src.zip
Changes:
- BAM QC: added chromosome names when drawing chromosome limits
- BAM QC: fixed fail when no mapped reads; add warning
- BAM QC: fixed computing coverage standard deviation (reported by Charlotte Peeters)
- BAM QC: by default duplicates (secondary alignments) are skipped if marked
- BAM QC: addded report for "OutOfMemory" error
- RNA-seq QC: added support for computing number of read pairs
- Counts QC: fix fail when sample name starts from number (reported by Alena Dobiasova)
- Documentation: updated BAM QC, RNA-seq QC
- Documnetation: added special solution regarding DISPLAY issue on Linux server (suggested by Roberto Spreafico)
Version 2.1 - March 18, 2015
qualimap_v2.1.zip
qualimap_v2.1_src.zip
Changes:
- BAM QC: added percentage of mapped reads with at least one insertion or deletion
- BAM QC: added an option to skip duplicates when running analysis (suggested by Johan Dalberg)
- RNA-seq QC: add text report of results (suggested by Lorena Pantano)
- BAM QC: fixed issue with inRegionReferenceSize outside of regions (reported by Tristan Carland)
- comp-counts: fixed bug when output file path is wrong (reported by Stephane Plaisance)
- RNA-seq QC: fixed issue with no-sorting required, improved statistics and input description (thanks to Priyanka Jain for report)
- RNA-seq QC: fixed issue when num reads equals zero
- RNA-seq QC: improved logging (implemented by Lorena Pantano)
- Feature reader: improved exception processing
- Fixed an issue with output folder when outformat is PDF
Version 2.0.2 - February 10, 2015
qualimap_v2.0.2.zip
qualimap_v2.0.2_src.zip
Changes:
- Compute counts: fixed issue with GTF file analysis and added support for single-end reads strand specificity (thanks to Roberto Spreafico for reports)
- BAM QC: added support of mismatches and indels in the text report (thanks to Nils for report)
- RNA-seq QC: fixed issue with loading GTF files with strange names (thanks to Haroon Kalam for report)
- RNA-seq QC: fixed crash when there are no junctions detected (thanks to François Lefebvre and Larry Willhelm for reports)
- Multi-BamQC: fixed issue with max coverage of BAM file supported
Version 2.0.1 - January 6, 2015
qualimap_v2.0.1.zip
qualimap_v2.0.1_src.zip
Changes:
- BAM QC: fixed problem with nucleotide content (thanks to Travis Collier)
- RNA-seq QC: fixed issue with chromosomes
- RNA-seq QC: add support for paired-end reads
- countsQC: fixed bug when population less than sample size
- Fixed issue with default outdir name
Version 2.0 - August 28, 2014
qualimap_v2.0.zip
qualimap_v2.0_src.zip
Changes:
- New mode: multi-sample BAM QC
- Counts QC: completely redesigned, add support for multi-sample input
- RNA-seq QC: add new plots (coverage across genebody, reads genomic origin, junction analysis)
- Command line interface improved
- BAM QC: changed order of plots
- BAM QC: fix insert size overflow
- BAM QC: add insert size info to plain text report
- BAM QC: fix bug with stats inside of regions
- BAM QC: performance improved for long genomes
- RNA-seq QC: fix default protocol
- Add utility script to create species annotations for Counts QC
- Add condtion to exit on error in main script (suggestion from Johan Dahlberg)
- Fix coverage quota in plain text report (bugfix from John Budde)
- Major documentation update
Version 1.0 - May 29, 2014
qualimap_v1.0.zip
qualimap_v1.0_src.zip
Changes:
- BAM QC: add computation of mismatches and error rate
- BAM QC: add new metrics for insert size
- BAM QC: contig coverage added to text report (patch from Johan Dahlberg)
- BAM QC: add option to output per-base coverage
- Compute counts: add full support for paired-end reads
- RNA-seq QC: add new plots and statistics
- Updated documentation
Version 0.8.1 - May 5, 2014 (a bug fix release)
qualimap_v0.8.1.zip
qualimap_v0.8.1_src.zip
Changes:
- Fixed bug with CountsQC and R version 3
- Fixed bug with reference size being computed twice in BamQC
Version 0.8 - March 5, 2014
qualimap_v0.8.zip
qualimap_v0.8_src.zip
Changes:
- Added new mode: "RNA-Seq QC"
- Fixed a number of bugs, including R-version issues and crash with insert size
Version 0.7.1 - April 19, 2013 (a bug fix release)
qualimap_v0.7.1.zip
qualimap_v0.7.1_src.zip
Changes:
- Fixed bug with "Coverage Across Reference" plot
- Fixed bug in BAM QC when regions don't have any coverage
Version 0.7 - April 10, 2013
qualimap_v0.7.zip
qualimap_v0.7_src.zip
Changes:
- Fixed bug in per chromosome coverage report (https://groups.google.com/d/msg/qualimap/AO_6111Gg1E/21SdvEWeAfUJ)
- Deletions are now properly computed when calculating coverage
- Fixed bug in renaming of tabs
- Added global parameter to set Rscript path
- Minor fixes in command line tools argument parsing
- Improved handling of discordant regions between the BED/GFF and BAM files in BAM QC
- Updated documentation
Version 0.6 - October 30, 2012
qualimap_v0.6.zip
qualimap_v0.6_src.zip
Changes:
- Fixed bug with small homopolymer indels estimation
- CIGAR flags "=" and "X" are now parsed properly in BAM QC
- BAM QC: added option to set minimum homopolymer size
- BAM QC: added option to open SAM files along with BAM files from GUI
Version 0.5 - July 25, 2012
qualimap_v0.5.zip
qualimap_v0.5_src.zip
Changes:
- BED format is now supported throughout application
- Raw data from BAM QC and Counts QC plots can be exported
- BAM QC: Added homopolymer indels estimation
- BAM QC: Added strand specificity calculation
- BAM QC: Added clipping profile and number of clipped reads statistics
- Compute counts: Added 5' to 3' prime bias calculation
- Allow to set java memory size from launching script
- Fixed problem with upperCoverageBound in Coverage Across Reference chart
- Fixed issue with insert size limits
- Added missing qualimap.bat to launch application on MS Windows
Version 0.4 - June 4, 2012
qualimap_v0.4_04-06-12.zip
Changes:
- Fixed problem with chromsome limits in Insert Size chart
- Fixed issue with "compute counts" when regions are having several intersecting reads
- Fixed crash with Coverage Histogram 0-50X for high coverage samples
- Fixed Coverage Histogram when minimal coverage is more than zero
- Fixed issue with GFF files, containing empty lines
Version 0.3 - May 18, 2012
qualimap_v0.3_18-05-12.zip
First public release.
