Releases: mikessh/migec
Releases · mikessh/migec
CLI and reporting fixes
- Fixes for
AssebleBatch
andCdrBlastBatch
- Allow partial report generation
Major update
- Finally implemented Diversity (D) segment extraction
- Speedup and search parameter optimization for CdrBlast
- Added minor alleles (from v1.1.2b pre-release)
- Minor bug fixes (pre-releases) and source code refactoring
Minor alleles included
- Added
CheckoutBatch
routine to handle samples demultiplex with Illumina indices - Added support for minor alleles, use
--all-alleles
option.NOTE to use alleles that are marked as pseudogenes, also use
--all-segments
option
Testing pre-release
v1.1.2a Changed syntax a bit to handle blank input/output
Several improvements and additions
- Chicken and duck alleles that were missing in IMGT, kindly provided by ZeZhong Li
- More control for overlapping reads in Checkout, better algorithm for overlap
- Ability to force MIG size threshold and collision filtering for all samples when running AssembleBatch
- Correct counting of MIGs when multiple files from the same sample are provided to CdrBlast
- Non-functional clonotype statistics reporting in FilterCdrBlastResults
- Minor fixes
Added support for several species
New references added:
Species | Gene |
---|---|
MacacaMulatta | TRB, IGK, IGH |
OryctolagusCuniculus | IGL, IGK, IGH |
RattusNorvegicus | IGL, IGH |
CanisLupusFamiliaris | TRB, TRG |
SusScrofa | IGL, IGK |
BosTaurus | TRD |
MusSpretus | IGL |
Adapter trimming feature
Adapter trimming and removal of (pG) trace of template-switching
Re-implemented BLAST usage
Should now run on Windows
Assembler collision filtering
Important for data with low PCR amplification, i.e. low number of reads per MIG
First release
v1.0.2 Create repo