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Releases: mikessh/migec

CLI and reporting fixes

27 May 16:55
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  • Fixes for AssebleBatch and CdrBlastBatch
  • Allow partial report generation

Major update

17 Feb 21:02
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  • 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

29 Jan 00:40
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  • 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

13 Jan 11:43
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v1.1.2a

Changed syntax a bit to handle blank input/output

Several improvements and additions

02 Sep 13:00
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  • 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

30 Jul 23:38
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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

27 May 13:19
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Adapter trimming and removal of (pG) trace of template-switching

Re-implemented BLAST usage

23 May 00:41
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Should now run on Windows

Assembler collision filtering

12 May 23:51
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Important for data with low PCR amplification, i.e. low number of reads per MIG

First release

14 Apr 12:51
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v1.0.2

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