Releases: milaboratory/mixcr
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 withanalyze 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 foranalyze
action (wrong aligner paramters were used before; datasets generated withanalyze
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 toanalyze
action (#454)- Minor fixes for
clonesDiff
andalignmentsDiff
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 asfeatureToAlign
for V geneVTranscriptWithP
instead ofVTranscriptWithout5UTRWithP
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 implementedanalyze amplicon
andanalyze 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 foralign
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
.
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
inexportAlignments
(#386) - Adds warning and fix for performance issue when
assemblePartial
misused for enriched library