MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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:
Powerful downstream analysis tools allow to obtain vector plots and tabular results for multiple measures. Key features include:
Other key features:
See full documentation at https://docs.milaboratories.com.
MiXCR is used by 8 out of 10 world leading pharmaceutical companies in the R&D for:
Widely adopted by academic community with 1000+ citations in peer-reviewed scientific publications.
brew install milaboratory/all/mixcr
to upgrade already installed MiXCR to the newest version:
brew update
brew upgrade mixcr
We maintain Anaconda repository to simplify installation of MiXCR using conda
package manager. To install latest stable MiXCR build with conda run:
conda install -c milaboratories mixcr
to install a specific version run:
conda install -c milaboratories mixcr=3.0.12
mixcr
package specifies openjdk
as a dependency, if you already have Java installed on your system, it might be a good idea to prevent conda from installing another copy of JDK, to do that use --no-deps
flag:
conda install -c milaboratories mixcr --no-deps
Official MiXCR Docker repository is hosted on the GitHub along with this repo.
Example:
docker run --rm \
-e MI_LICENSE="...license-token..." \
-v /path/to/raw/data:/raw:ro \
-v /path/to/put/results:/work \
ghcr.io/milaboratory/mixcr/mixcr:latest \
align -s hs /raw/data_R1.fastq.gz /raw/data_R2.fastq.gz alignments.vdjca
The docker repo provides pre-built docker images for all release versions of MiXCR starting from 1.1. Images come in two flavours: "mixcr only" (i.e tag 4.0.0
) and co-bundled "mixcr + imgt reference" (i.e. tag 4.0.0-imgt
), for the latter please see the license note below. All bundled versions before and including 4.0.0
contain IMGT reference version 202214-2
from here, this might be different from the images from the previous official docker registry on Docker Hub (which is now deprecated and planned for removal).
See docker packages page for the full list of tags including development builds.
There are several ways to pass the license for mixcr when executed inside a container:
Using environment variable:
docker run \
-e MI_LICENSE="...license-token..." \
....
Using license file:
docker run \
-v /path/to/mi.license:/opt/mixcr/mi.license:ro \
....
If it is hard to mount mi.license
file into already populated folder /opt/mixcr/
(i.e. in Kubernetes or with other container orchestration tools), you can tell MiXCR where to look for it:
docker run \
-v /path/to/folder_with_mi_license:/secrets:ro \
-e MI_LICENSE_FILE="/secrets/milicense.txt" \
....
New docker images define mixcr
startup script as an entrypoint of the image, compared to the previous docker repo where bash
was used instead. So, what previously was executed this way:
docker run ... old/mixcr/image/address:with_tag mixcr align ...
now will be
docker run ... new/mixcr/image/address:with_tag align ...
For those who rely on other tools inside the image, beware, new build relies on a different base image and has slightly different layout.
mixcr
startup script is added to PATH
environment variable, so even if you specify custom entrypoint, there is no need in using of full path to run mixcr
.
Images with IMGT reference library contain data imported from IMGT and is subject to terms of use listed on http://www.imgt.org site.
Data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)."
References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001); Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003); Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text, Lefranc, M.-P. et al., Nucleic Acids Research 2009 37(Database issue): D1006-D1012; doi:10.1093/nar/gkn838 Full text.
PATH
variable
mixcr
script to your bin
folderTo run MiXCR one needs a license file. MiXCR is free for academic users with no commercial funding. We are committed to support academic community and provide our software free of charge for scientists doing non-profit research.
Academic users can quickly get a license at https://licensing.milaboratories.com.
Commercial trial license may be requested at https://licensing.milaboratories.com or by email to [email protected].
To activate the license do one of the following:
mi.license
to
~/.mi.license
~/mi.license
mixcr.jar
fileMI_LICENSE_FILE
environment variablemi.license
content to MI_LICENSE
environment variablemixcr activate-license
and paste mi.license
content to the command promptSee usage examples and detailed documentation at https://docs.milaboratories.com
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] .
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.
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.
(Files referenced in this paper can be found here.)
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)