MiXCR v3.0.7

Major changes

• Fixes clone oversplitting in assembleContigs in noizy (e.g. single-cell) data with substanial fraction of sequences with errors in CDR3
• Fixes wrong alignment-scoring-based filtering in pre-clustering procedure
• Fixes rare bug in export of imputed gene feature sequences

Minor changes

• Now -OseparateByV=false and similar overrides works with analyze shotgun (issue #512)
• Better error message for mutation extraction from alignment-attached gene features

MiXCR is free for non-profit use only (see LICENSE for details)!
For commercial use please contact licensing@milaboratory.com.

MiXCR v3.0.6

• Fixes V/J/C oversplitting issue in noizy data
• Additional fix for empty block exception in assemble action
• Fixed filtering by chain in export in analyze action with default settings
• Special symbols for NaN in report now outputted as "NaN" string

MiXCR is free for non-profit use only (see LICENSE for details)!
For commercial use please contact licensing@milaboratory.com.

MiXCR v3.0.5

• Fixed writing empty block exception arising with empty input files and in several other situations

MiXCR is free for non-profit use only (see LICENSE for details)!
For commercial use please contact licensing@milaboratory.com.

MiXCR v3.0.4

• Fixed problem with possibly incorrect clone-to-alignment mapping and clonotype sorting. The problem manifests itself in rare cercumstances, with -OseparateByV/J/C=true (special thanks to Victor Greiff @GreiffLab for finding the bug and helping with testing)
• Fixes exception while reading alignments from clna files (thanks to Dr. Ma @JohnMCMa for finding the bug and providing the data to reproduce it)
• Integration with new MiLib abstraction for CLI, to automatically infer when reanalysis is nedded and when not (this mechanism extracts paramteres from the target files, and checks if current command line sets the same options, if the options are the same, mixcr skips the step, otherwize restarts the analysis)
• Report for the assemble command now contains chain distribution statistics
• analyze command now is case-insensitive for all options like --starting-material
• Fixed exception arising in rare cases with sequence imputation on the export step

MiXCR is free for non-profit use only (see LICENSE for details)!
For commercial use please contact licensing@milaboratory.com.

MiXCR v3.0.3

• ⚠️ Major fix for analyze action (wrong aligner paramters were used before; datasets generated with analyze action should be reanalyse)
• Also several minor fixes to the overal logic of analyze
• Fix for exported clonotype tables for specific receptor chains in analyze (#454)
• --no-export option added to analyze action (#454)
• Minor fixes for clonesDiff and alignmentsDiff actions

MiXCR is free for non-profit use only (see LICENSE for details)!
For commercial use please contact licensing@milaboratory.com.

MiXCR v3.0.2

• Additional fix for error in exportAlignments / exportClones with repeated non-parametrized options
• Added support for affine alignments in assembleContigs

MiXCR v3.0.1

• This fixes problem with repeated CLI options in export
• VRegionWithP now is used as featureToAlign for V gene
• VTranscriptWithP instead of VTranscriptWithout5UTRWithP used for RNA-Seq parameters
• Rename -sequence to -targetSequences and -quality to -targetQualities in export #298
• Minor cosmetics for clone ordering #401

MiXCR v3.0

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

• fixes for #292 #280 #279 #208 #203 #421
• --noMerge option renamed to --no-merge in assemble action

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.

MiXCR v2.1.12

• Fixes rare inconsistency in behaviour between paired-end and single-end aligners, clone assembler and partial sequence assembler in respect to target D gene set selection based on the chains on V, J and C genes (#408)

MiXCR v2.1.11

Major changes

• Major review of affine alignment algorithms

Minor changes

• Fix for MiXCR script for Java 9+
• Fix for exception with no D hits in -dIdentityPercent in exportAlignments (#386)
• Adds warning and fix for performance issue when assemblePartial misused for enriched library