Skip to content

MiXCR v4.0
Compare
Choose a tag to compare
@dbolotin dbolotin released this 10 Jun 01:22
· 2644 commits to develop since this release
v4.0.0
c604f8d

Comprehensive support for Single-Cell and Molecular barcodes

  • flexible and fast pattern matching engine to parse barcodes from the data; allows to fit the pipeline to any
    commercially available or in-house wet lab protocol with molecular or/and cell barcodes
  • error correction in barcode sequences
  • two cooperating UMI and/or Cell-barcode-based steps for clonal sequence reconstruction:
    • consensus assembly (i.e. for well-framed amplicon sequencing)
    • contig assembly (i.e. for 10x-like enzymatically fragmented data)
  • tag information preserved on all analysis steps and extensive QC reports are generated throughout the pipeline,
    providing maximal visibility into analysis performance and giving a powerful tool for wet lab issues investigation

See the following usage examples:

Downstream analysis

Set of powerful downstream analysis features with the ability to export postanalysis results in tabular format and vector plots with various statistical comparisons.

  • Ability to group samples by metadata values and compare repertoire features between groups
  • Comprehensive repertoire normalization and filtering
  • Statistical significance tests with proper p-value adjustment
  • Repertoire overlap analysis
  • Vector plots output (.svg / .pdf)
  • Tabular outputs

See the following usage guide:

Overlap browser

Added command exportClonesOverlap allowing to efficiently build and export overlap of the arbitrary number of clonesets.

Major rework of contig assembly algorithm

  • significantly increased accuracy and stability
  • works with or without molecular or cell barcodes
  • can be applied to (sc)RNASeq data with reasonable IG/TCR coverage to reconstruct long sequence outside the CDR3

Export in AIRR format

  • multiple options to export alignment or clonal data in AIRR format
  • provides better compatibility with 3rd-party tools from AIRR community (see also RepSeq.IO feature for generation of fasta libraries with IMGT-like gaps from repseqio formatted references)

See here for usage example.

Other improvements and changes

  • new built-in reference library with new species and newest genome based library for human
    (see changelog here)
  • complete rewrite of IO for intermediate files (much faster IO with parallel serialization and deserialization,
    more compact files - each block is compressed with LZ4, versatile random access features provides additional speedup)
  • faster hash-based external (file-based) sorting algorithm for alignment and other regrouping tasks in UMI/Single-cell
    related tasks and operations requiring alignment to clone mapping
  • input sequence quality-score based trimming enabled by default
  • support for human-readable alignments export from *.clna files by clone index
  • all steps are cleaned-up to be completely pure, i.e. for the same input, output will always be byte-to-byte equal
    (no analysis date or other variable pieces of information leaks to the output files)
  • more stable amino acid and combined amino acid plus nucleotide mutations export
  • slight default analysis parameter optimization

Obtaining a license file

MiXCR requires a license file to run. Academic users with no commercial funding can quickly obtain a MiXCR license for free at https://licensing.milaboratories.com/. We are committed to support academic community and provide our software free of charge for scientists doing non-profit research. Commercial trial license can be requested at https://licensing.milaboratories.com or by email to [email protected].

For details see: https://mixcr.com/mixcr/getting-started/milm/

Assets 3
Loading