Apr 17, 2020
*Added ability to use custom organism.
*Added ability to extend J gene alignment at 3’ end.
*Added the AIRR complete_vdj field.
*Deleted parameters that are used for standard BLAST but not for IgBLAST.
Jan 21, 2020
*Added support for the FWR4 annotation.
*The previous “-penalty” parameter was renamed as V_penalty to be consistent with other IgBLAST penalty options
*Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters
*Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.
Apr 29, 2019
Making AIRR format more consistent with AIRR specs including changing undefined type (NON, N/A) to empty string, not appending “reversed” to seqid when query is in reversed orientation, using standard locus names such as IGH, TRB instead of traditional VH, VB etc.
Loosening criteria to show CDR3 end by allowing the first FWR4 base to be missing.
Bug fix: Restoring seqid for no result case in AIRR rearrangement format. Printing IgBlast version number instead of Blast version number with -version option.
Mar 7, 2019
- Release 1.13.0
Determine the V gene reading frame from the end of FWR3 region instead of end of V gene. This is to allow proper determination of the frames for rearrangements that have insertions or deletions near the V gene end.
Increase allowed distance between V gene end and J gene start to 225 bp to allow detection of ultra long D/N region.
- Package the edit_imgt_file.pl script, the internal_data and optional_files folders into the IgBlast release such that it is easy for u ser to install.
Nov 26, 2018
Increase allowed distance between V gene end and J gene start positions (from 90 bp to 150 bp) as well as between V gene end and D gene start positions (from 55 to 120 bp) to accommodate extremely long VDJ junctions found in some antibodies.
Oct 25, 2018
Change the 0-based coordinate system to 1-based coordinate system in AIRR format (with -outfmt 19 parameter) for sequence start positions per the new AIRR Rearrangement Schema ( http://docs.airr-community.org/en/latest/datarep/rearrangements.html ).
Aug 24, 2018
Fix some processes not exiting under cpu full load condition
April 30, 2018
Adding the AIRR rearrangement tabular format
Sept 22, 2017
Re-engineered multi-threading mechanism which significantly shortens the processing time. Default t o use 4 threads.
Added ability to accept the SRA accession directly as query input.
Lower the default nucleotide mismatch penalty values for finding D and J genes (from -4 to -2 and f rom -3 to -2, respectively). This is to better accommodate moderately mutated sequences.
April 19, 2017
- Make nucleotide overlaps at VDJ junctions an option (-allow_vdj_overlap) and default is set to no o verlap allowed. Previous versions were hard-coded to allow nucleotide overlaps at VDJ junctions. *Use alignment length instead of percent identity as tiebreaker for hits with identical blast scores .
- Allow custom J gene mismatch penalty.
- Add CDR3 start and stop to sub-region table
Oct 26, 2016
- Release 1.6.1
- Added clonotype report
- Enabled multi-threading option -num_threads
April 25, 2016
- Release 1.5.0
- Added CDR3 annotation
- Added option for extending at 5’ side
- Default to IMGT region (was Kabat previously)
July 17, 2014
- Release 1.4.0
- Added capability to analyze monkey sequences.
February 19, 2014
- Release 1.3.0
- Better handling of non-Ig sequences
- Include makeblastdb binary with pre-compiled releases