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MiXCR v2.1
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@dbolotin dbolotin released this 06 Feb 16:57
· 3348 commits to develop since this release
v2.1
7c4dcd4

DOI

⚠️ -defaultAnchorPoints fields have changed. Values for array elements with indices 11, 12, 15, 16 now represents number of 3’/5’ deletions or P-segment length for V, D, J genes. See documentation for more information.

⚠️ Default output format in exportClones and exportAlignments have changed. Scripting-friendly header column names are now used by default. Use -v option for previously default format.

  • Major review of all analysis steps for non-enriched libraries (RNA-Seq, etc...). Efficiency of TCR/IG extraction substantially improved (according to our benchmarks, efficiency is highest among all tools available for RNA-Seq repertoire extraction known to date; successfully work even for 48+48 RNA-Seq data). Zero false-positive alignments and false-overlaps detected.
  • Additional round of alignment for V gene in paired-end reads aligner (improve efficiency and accuracy for some boundary cases; negligible impact on analysis speed).
  • New action extendAlignments to extend TCR alignments with uniquely defined V and J genes but not fully covering CDR3 sequence.
  • Scripting-friendly export format now used by default. Use -v to return to column names with spaces.
  • Information on the number of deleted nucleotides / size of P-segment for V, D, and J genes now is explicitly exported in -defaultAnchorPoints field (see docs for more info).
  • Many small fixes and enhancements.
  • Correct marks for P-segment of J gene in exportAlignmentsPretty and exportClonesPretty
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