milaboratory / mixcr

• Built-in reference library upgraded to v1.6 (see changes)
• Additional mixcr script optimizations for docker

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

• Fixes exception in assemble for multi-assembling-feature cases with zero length sequences
• Fixes empty FR3 imputed sequence in cases with zero assembled nucleotides on the 5' side of CDR3
• MiXCR execution script optimized for Docker (Java 11 is recommended for running MiXCR in container environment)
• Other fixes for MiXCR script

Starting from this release we will maintain Official MiXCR Docker Image.

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

• Fixes NPE in very rare cases with incompatible V gene selection for assembleContigs in case of partially annotated gene libraries
• Several fixes for sequence imputation algorithm in exportAlignments / exportClones

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

• Fixed wrong behaviour with score-based pre-filtering in split-by-V/J=true cases
• Chain usage statistics added to align and assemble JSON reports
• Fixed rare IndexOutOfBounds exception in -nFeatureImputed ...
• Added shortcut for --json-report = -j
• Sanity check for common mistake in analyze parameters

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

Major changes

• Alignments are forced to the corresponding edge if the same V/J gene is detected in the opposite PE read mate
• Average quality threshold (-OaverageQualityThreshold=...) in assembleContigs increased to 20
• Added exportAlignmentsForClones action
• All indels in homopolimeric stretches are now shifted left in all alignment algorihtms
• Smarter base V/J/C hit selection in assembleContigs
• Read quality trimming (see help for --trimming-window-size and --trimming-quality-threshold options in align) (disabled by default until 3.1)
• Fix exception in -mutationsDetailed and similar export options
• Fixes in step skipping logic in analyze (additional automatic parameter adjustment for VDJC libraries covering only VRegion)
• Several more fixes for assembleContigs

Minor changes

• Fixes incorrect numbers in assemble report
• Fix for filterAlignmentsAction

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

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.

• 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.

• 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.

• 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.