mixcr

❗ Breaking changes

• Starting from version 4.7.0 of MiXCR, users are required to specify the assembling feature for all presets in cases where it's not defined by the protocol. This can be achieved using either the option --assemble-clonotypes-by [feature]or --assemble-contigs-by [feature] for fragmented data (such as RNA-seq or 10x VDJ data). This ensures consistency in assembling featu...

🖇️ Combined Heavy+Light Somatic Hypermutation Trees from Single-Cell data

• A special step is added in findShmTrees to combine heavy and light SHM trees utilizing information added to clonotypes by groupClones command. Nodes in resulting tree will contain both light and heavy chains. If there is no connection to a clone from a companion chain, a reconstructed sequence will be added. -...

🚀 New features

Multi-chain clone assembly for single-cell data

Now MiXCR calculates Heavy-Light antibody and Alpha-Beta and Gamma-Delta TCR combined clones for single-cell data. Two new commands were introduced to enable this functionality:

• groupClones: calculates multi-chain clones from assembled clonotypes and writes result in a binary format;
• exportCloneGroups: expor...

🚀 New features

• Two-fold align step speedup for most of the protocol-specific presets (see the list below)
• Import tags from sequence headers by parsing its content with regular expressions
• Highly optimized generic presets for amplicon/rna-seq sequence by long-read sequencers such as Pacific Biosciences and Oxford Nanopore: generic-ont, generic-ont-with-umi, generic-pacbio, `...

🐞 Bug fixes

• resolves issue encountered while executing MiXCR on Windows OS