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MiXCR v3.0
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@dbolotin dbolotin released this 23 Oct 01:35
· 3120 commits to develop since this release
v3.0
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dbolotin Dmitry Bolotin
GPG key ID: 537CA9922FCED403
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Learn about vigilant mode.
Major changes
  • New command assembleContigs for assembling longest possible contig TCR/IG receptor sequences from several intersecting sequences containing clonal sequence. E.g. assemble all possible sequence information outside CDR3.
  • New command analyze for running optimized mixcr pipelines with one single command. Two pipelines which cover most practical cases are implemented analyze amplicon and analyze shotgun.
  • New file format .clna for storing clones with alignments including alignments <> clones mapping
  • Complete refactoring of command line interface
  • New option --resume for resuming aborted / partially completed execution
  • Implemented -nFeatureImputed and -aaFeatureImputed to export gene feature sequences imputing unavailable regions from germline sequences up to the full feature sequecn (marking imputed regions lowercase)
  • LZ4 based compression for .vdjca/.clna files, 3 ~ 4 fold file size reduction (built into file formats, enabled by default)
  • Species option --species is now mandatory #342
  • Removed --chains option for align action #292
  • Added export field -positionInReference
  • Now export fields like -nMutationsRelative supports alignment-attached gene features (e.g. this allows to export all mutations of V gene inside CDR3 sub-regions: -nMutationsRelative VCDR3Part VRegionWithP)
  • Now align action prints library-level warnings and citation notice
  • Refactored command line interface of exportReadsForClones
  • Dropped support for Java 7
Minor changes
Installation

To install this version with Homebrew use mixcr3 formulae. If you have previous mixcr version installed with homebrew, unlink it before installation:

brew unlink mixcr

and install MiXCR 3.0

brew install mixcr3

We created separate formulae for the new version, because it contains too many breaking changes and may interrupt normal work if update from MiXCR 2.* to MiXCR 3.* happen automatically during brew upgrade.

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