milaboratory / Mixcr

Overview

MiXCR is a universal software for fast and accurate analysis of raw T- or B- cell receptor repertoire sequencing data.

• Easy to use. Default pipeline can be executed without any additional parameters (see Usage section)

• TCR and IG repertoires

• Following species are supported out-of-the-box using built-in library:

  • human
  • mouse
  • rat (only TRB and TRA)
  • ... several new species will be available soon

• Efficiently extract repertoires from most of (if not all) types of TCR/IG-containing raw sequencing data:

  • data from all specialized RepSeq sample preparation protocols
  • RNA-Seq
  • WGS
  • single-cell data
  • etc..

• Has optional CDR3 reconstruction step, that allows to recover full hypervariable region from several disjoint reads. Uses sophisticated algorithms protecting from false-positive assemblies at the same time having best in class efficiency.

• Assemble clonotypes, applying several error-correction algorithms to eliminate artificial diversity arising from PCR and sequencing errors

• Clonotypes can be assembled based on CDR3 sequence (default) as well as any other region, including full-length variable sequence (from beginning of FR1 to the end of FR4)

• Assemble full TCR/Ig receptor sequences

• Provides exhaustive output information for clonotypes and per-read alignments:

  • nucleotide and amino acid sequences of all immunologically relevant regions (FR1, CDR1, ..., CDR3, etc..)
  • identified V, D, J, C genes
  • nucleotide and amino acid mutations in germline regions
  • variable region topology (number of end V / D / J nucleotide deletions, length of P-segments, number of non-template N nucleotides)
  • sequencing quality scores for any extracted sequence
  • several other useful pieces of information

• Completely transparent pipeline, possible to track individual read fate from raw fastq entry to clonotype. Several useful tools available to evaluate pipeline performance: human readable alignments visualization, diff tool for alignment and clonotype files, etc...

Installation / Download

Using Homebrew on Mac OS X or Linux (linuxbrew)

brew install milaboratory/all/mixcr

to upgrade already installed MiXCR to the newest version:

brew update
brew upgrade mixcr

Docker

See official Docker Image.

Manual install (any OS)

• download latest stable MiXCR build from release page
• unzip the archive
• add resulting folder to your PATH variable
  • or add symbolic link for mixcr script to your bin folder
  • or use MiXCR directly by specifying full path to the executable script

Requirements

• Any OS with Java support (Linux, Windows, Mac OS X, etc..)
• Java 1.8 or higher

Usage

See usage examples in the official documentation https://mixcr.readthedocs.io/en/master/quickstart.html

Documentation

Detailed documentation can be found at https://mixcr.readthedocs.io/

If you haven't found the answer to your question in the docs, or have any suggestions concerning new features, feel free to create an issue here, on GitHub, or write an email to [email protected] .

Build

Requirements:

• Maven 3 (https://maven.apache.org/)

To build MiXCR from source:

• Clone repository

  git clone https://github.com/milaboratory/mixcr.git
  

• Refresh git submodules

  git submodule update --init --recursive
  

• Run build script. First build may take several minuties to download sequences for built-in V/D/J/C gene libraries from NCBI.

  ./build.sh
  

License

Copyright (c) 2014-2019, Bolotin Dmitry, Chudakov Dmitry, Shugay Mikhail (here and after addressed as Inventors) All Rights Reserved

Permission to use, copy, modify and distribute any part of this program for educational, research and non-profit purposes, by non-profit institutions only, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies.

Those desiring to incorporate this work into commercial products or use for commercial purposes should contact MiLaboratory LLC, which owns exclusive rights for distribution of this program for commercial purposes, using the following email address: [email protected].

IN NO EVENT SHALL THE INVENTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE, EVEN IF THE INVENTORS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE INVENTORS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE INVENTORS MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE SOFTWARE WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.

Cite

• Dmitriy A. Bolotin, Stanislav Poslavsky, Igor Mitrophanov, Mikhail Shugay, Ilgar Z. Mamedov, Ekaterina V. Putintseva, and Dmitriy M. Chudakov. "MiXCR: software for comprehensive adaptive immunity profiling." Nature methods 12, no. 5 (2015): 380-381.

• Dmitriy A. Bolotin, Stanislav Poslavsky, Alexey N. Davydov, Felix E. Frenkel, Lorenzo Fanchi, Olga I. Zolotareva, Saskia Hemmers, Ekaterina V. Putintseva, Anna S. Obraztsova, Mikhail Shugay, Ravshan I. Ataullakhanov, Alexander Y. Rudensky, Ton N. Schumacher & Dmitriy M. Chudakov. "Antigen receptor repertoire profiling from RNA-seq data." Nature Biotechnology 35, 908–911 (2017)

Files referenced in original paper

Can be found here.