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MiXCR v1.8
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@dbolotin dbolotin released this 21 Jun 09:32
· 3663 commits to develop since this release
v1.8
f1183c4

⚠️ All users are recommended to upgrade to MiXCR 1.8.1. Users who analyse their data with clusterization turned off (-OcloneClusteringParameters=null) are recommended to reanalyse their data with newer MiXCR version.

Major changes
  • Assembler of partial reads allows to assemble CDR3s from several short reads: final puzzle piece for high quality repertoire data extraction from RNA-Seq data
  • Added support for P-segments; new gene features VPSegment, DLeftPSegment, DRightPSegment, JPSegment now available both in exportAlignments and exportClones; feature is enabled by default
  • Added new anchor points to encode information about P-segment positions
  • Clone assembler now can separates clones with different V/J/C genes but same clonal sequence (e.g. CDR3); this behaviour is turned off by default (see -OseparateByV/J/C in assemble action parameters to turn it on)
  • Quality aggregation algorithm in assembler changed (see description of assemble procedure)
  • Added clone filtration step: filter clones with low quality clonal sequence (see -OminimalQuality parameter)
  • Added new action alignmentsDiff: run as mixcr alignmentsDiff file1.vdjca file2.vdjca report.txt to find difference between two .vdjca files
  • Following export fields added: -vFamily, -vFamilies (same for D/J/C)
  • Added new options in align: --not-aligned-R1 and --not-aligned-R2 for exporting not aligned reads at alignment step (useful for troubleshooting of raw data glitches / analysis parameters)
  • Alignment seed is now fixed in order to have completely equal results from run to run on the same dataset
  • Added option -e/--cdr3-equals to exportAlignmentsPretty action
  • Added option -v/--write-all to align action
  • Action exportReads renamed to exportReadsForClones
  • Added exportReads action to re-export raw reads from *.vdjca file; useful to filter TCR/IG containing reads
  • Added new -l/--filter-locus option in exportClones action to limit the list of exported clones by specified locus
  • Added new -q/--minimal-clone-fraction and -c/--minimal-clone-count options in exportClones action to filter the list of exported clones by their fraction of reads number
Minor changes
  • Refactoring of report in assemble action: better descriptions, fixes and new informative lines
  • Human-readable error messages for illegal analysis options with IMGT reference
  • Added new export field: -vBestIdentityPercent and -vIdentityPercents (-j..., -c... in the same way)
  • Now IMGT import script produces more useful information
  • Added human-readable error message for unknown species
  • Better layout of anchor point marks in exportAlignmentsPretty
  • Optional output of read description lines (if present in vdjca file) in exportAlignmentsPretty
Assets 3
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