MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. It works with any kind of sequencing data:

Bulk repertoire sequencing data with or without UMIs
Single cell sequencing data including but not limited to 10x Genomics protocols
RNA-Seq or any other kind of fragmented/shotgun data which may contain just a tiny fraction of target sequences
and any other kind of sequencing data containing TCRs or BCRs

Powerful downstream analysis tools allow to obtain vector plots and tabular results for multiple measures. Key features include:

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

Other key features:

Clonotype assembly by arbitrary gene feature, including full-length variable region
PCR / Sequencing error correction with or without aid of UMI or Cell barcodes
Robust and dedicated aligner algorithms for maximum extration with zero false-positive rate
Supports any custom barcode sequences architecture (UMI / Cell)
Human, Mice, Rat, Spalax, Alpaca, Monkey
Support IMGT reference
Barcodes error-correction
Adapter trimming
Optional CDR3 reconstruction by assembling overlapping fragmented sequencing reads into complete CDR3-containing contigs when the read position is floating (e.g. shotgun-sequencing, RNA-Seq etc.)
Optional contig assembly to build longest possible TCR/IG sequence from available data (with or without aid of UMI or Cell barcodes)
Comprehensive quality control reports provided at all the steps of the pipeline
Regions not covered by the data may be imputed from germline
Exhaustive output information for clonotypes and alignments:
- nucleotide and amino acid sequences of all immunologically relevant regions (FR1, CDR1, ..., CDR3, etc..)
- identified V, D, J, C genes
- comprehensive information on nucleotide and amino acid mutations
- positions of all immunologically relevant points in output sequences
- and many more informative columns
Ability to backtrack fate of each raw sequencing read through the whole pipeline

License

Copyright (c) 2014-2022, MiLaboratories Inc. All Rights Reserved

Before downloading or accessing the software, please read carefully the License Agreement available at:

https://github.com/milaboratory/mixcr/blob/develop/LICENSE

By downloading or accessing the software, you accept and agree to be bound by the terms of the License Agreement. If you do not want to agree to the terms of the Licensing Agreement, you must not download or access the software.

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