Skip to content

MiXCR v4.1.1
Compare
Choose a tag to compare
@github-actions github-actions released this 11 Nov 14:55
v4.1.1
3418ff5
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

Overview

With this release we continue extending the set of supported single-cell protocols by adding new ready-to-use presets to our collection. Additionally to newly supported protocols and features required for their reliable processing this release comes with many usability optimizations and stability improvements. See details below:

Major changes

  • presets for analysis of all types of BD Rhapsody data (see docs for the list of supported kits)
  • analysis of data produced by single-cell protocol described in Han et al. (2014) (see docs)
  • special presets for exom data analysis exom-cdr3 and exom-full-length
  • initial support for overlap-extension-based chain pairing protocols
  • possibility to export groups of similar columns specifying single option (like -allAAFeatures <from_reference_point> <to_reference_point>)
  • user-friendly alternative for -uniqueTagsCount - -allUniqueTagsCount; allows to export counts of unique tag combinations (useful for protocols with multiple CELL and UMI barcodes)
  • new "by sequence" filters for all somatic hypermutation trees (SHMT) exports
  • new weighted auto-threshold selection and complementary metric histogram aggregation modes (i.e. y-axis on reads-pre-UMI plots now can show number of reads instead of number of UMIs)
  • detected allelic variants are now can also be exported in fasta format right from the findAlleles command
  • better algorithm for seed sequence selection in consensus assembly routine in assemble; increases productive consensus count for cases with multi-variant tag groups (i.e. birthday paradoxes in UMI data or single-cell data analysis without UMIs)

Minor changes:

  • minor adjustments for existing presets
  • many CLI and parameter validation fixes, more human-readable error messages, better protection from common input errors
  • support for preset-embedded tag whitelists for protocols with small number of barcode variants
  • options --use-local-temp, --threads, --not-aligned-R1(R2) and --not-parsed-R1(R2) are now available in analyze, additionally to individual step commands
  • bugfix for imputation in export for compound gene features
  • other minor fixes and enhancements
Assets 3
Loading