MiXCR v2.1

⚠️ -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

MiXCR v2.0.4

Major changes

• Fix for NPE in -nMutations ... -aaMutations ...
• Correct visualization of D gene P segments in exportAlignmentsPretty

Minor changes

• Fix for error in export when fields are given in the file

MiXCR v2.0.3

Major changes

• User-friendly export of mutations in germline sequences: nucleotide, amino-acid and detailed (provides means to link nucleotide mutations with resulting amino-acid mutations; e.g. it allows to easy differentiate between sense and nonsense nucleotide mutations). Mutations can be exported for any gene feature (e.g. FR3) realtive to any gene feature (e.g. VRegion).
• Fix for NPE in assemble action invoked with -OmaxBadPointsPercent=0
• Support for Linux free version 3.3.10 in mixcr wrapper script (now MiXCR runs on Centos 7.2, Ubuntu 16.04.1)
• Unified way for gene feature translation (frame is inferred using closest reference point known to be in-frame)

Minor changes

• fix for wrong filtering of stop codons in case of featuresToAlign with non-coding regions
• Backward compatibility option --diff-loci in align action

MiXCR v2.0.2

• Fixes NPE in exportClones action

MiXCR v2.0.1

Major changes

• Fixes problem with absent library search folders
• Added action exportClonesPretty, that prints well-formatted alignments for segments and clonal sequence
• Human readable report for assemblePartial action
• Additional micro-filtering step for alignment hits to exclude wrong chain hits
• RepSeq.IO: fixes bug when MIXCR fails to resolve partial library name for files without .gz extension
• Print warning when using java version <= 7
• RepSeq.IO library updated to v1.1 (fixed human IGHV4-61 and IGLC7, IGLC3)

Minor changes

• Statistics about chains usage is added to align and assemble reports
• Added chains (--chains or -c option) filter for exportAlignments
• Execution time is now printed in reports

MiXCR v2.0

⚠️ This MiXCR version has no backward compatibility with *.vdjca / *.clns files produced by previous versions.

Major changes

• New JSON-based reference library format (see RepSeq.IO)
• Complete review of V/D/J/C gene library (see repository)
• New simplified method to import IMGT library (see documentation)
• All --loci options replaced with --chain (-l -> -c)
• Removed option --diff-loci at align step
• Added -OallowChimeras=true / false option at align step (better algorithm than was with --diff-loci)
• Removed: option -u/--functional-only in align action
• Many small fixes

Minor changes

• Improved report content with absolute values for all rows and additional version info
• Now report with run statistics is additionally printed to stdout
• Execution time information added to report

MiXCR v1.8.3

Major changes

• Bugfix: C alignment now will be performed in R2 only for alignments with V gene in R1 (affects only align with -OallowPartialAlignments=true)
• Fix for wrong hits filtration in case of -OallowPartialAlignments=true
• Alignment-to-clone index rewritten from scratch (see -i / --index option in assemble)
• MapDB dependency removed
• Fixes occasional NullPointerException during reading of alignemnt-clone index
• Fixes NullPointerException with -descrR2 in exportAlignments
• Better wording for command options descriptions in built-in help (printed by mixcr -h)

Minor changes

• Additional fixes for reproducibility of run-to-run results (internal rounding of float hit scores, additional reseeding of random seed in mapping).

MiXCR v1.8.2

• Fixed floatingRightBound=false for rna-seq alignment parameters
• Added new action filterAlignments
• Fixed wrong output for gene family export columns
• Several fixes for alignment report
• Default value for qualityMergingAlgorithm for paired-end merger changed to MaxSubtraction
• Fixed NPE / IllegalArgumentException in case of complex assemblingFeatures

MiXCR v1.8.1

• Revert quality filtering/mapping algorithm to MiXCR 1.7.x
• Added different quality aggregation algorithms for assemble (Average, Min, Max, MiniMax) option -OqualityAggregationType=Max
• Added clonesDiff action to calculate descriptive statistics of difference between two samples
• Fixed wrong anchor point positions in Macaca mulatta IGL reference imported using importFromIMGT.sh script
• MiXCR returns exit code 1 if program terminated with error
• Automatic correction of -OvParameters.geneFeatureToAlign in align action for some cases (e.g. imported IMGT reference and rna-seq parameters)

MiXCR v1.8

⚠️ 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