Skip to content

MiXCR v4.3.0
Compare
Choose a tag to compare
@github-actions github-actions released this 17 Mar 16:46
v4.3.0
96be4ef

Key changes

  • Improved Otsu's method with less stringency for automated histogram thresholding for barcoded data. It allows to recover more "good" UMI groups. The old filter was replaced by new one in all presets for airr-seq and single cell V(D)J protocols that utilize UMI: Cellecta, Milaboratories, NEB, Qiagen, Takara, 10x Genomics, BD, Singleron.
  • New group filter operators allowing to mix thresholds form multiple operators, taking lowest or highest value and applying it. This allows to create more universal filtering strategies, robust to edge cases like undersequencing of barcodes.
  • Added default fallback threshold for UMI filtering: if automated UMI thresholding leaves less than 85% of reads, then MiXCR will preserve UMIs to always keep minimum 85% of reads.

Presets

  • New preset for Seq-Well VDJ data
  • New presets for NEBNext® Immune Sequencing Kit TCR and BCR profiling for data with both TCR and BCR.
  • Improved Takara human TCR and BCR presets

Reference Library

  • New IGHV genes added to human reference: IGHV3-30-3, IGHV4-30-4, IGHV1-69-2, IGHV2-70D, IGHV3-30-5
  • IGHV1-69D renamed to IGHV1-69

Minor improvements

  • Threshold rounding in cumtop and top-n filters
  • Support of sequence-end token ($) in tag pattern matching algorithm
  • Added discardAmbiguousNucleotideCalls parameters for contig assembly
  • Added field -cellId in commands exportClones and exportAlignments
  • Added fields cell_id, umi_count and consensus_count to exportAirr command
  • Better text descriptions in align and assemble reports
  • exportAirr command now split clones by cells if there is cell barcodes in the data
  • Replace analyze options --not-aligned-.. and --not-parsed-.. with one option --output-not-used-reads
  • Fix comma-separated chains input in postanalysis --chainsoption
  • Split column with tagValue (like tagValueCELL) to two columns: tagValue<tag_name> and tagQuality<tag_name>
  • Support of system proxy settings for license
  • # character now can be used to separate groupName from group matcher in file expansion mechanist (additionally to :), allowing multi-sample analysis on Windows
  • Fixed usage of composite features for --assemble-contigs-by
  • Removed some restrictions for possible combinations of gene features used in analysis and export
  • Fixed behaviour of empirical alignment assignment in assemble if --write-all was used in align
Assets 3
Loading