Quick Links Interactive Job Documentation

Immcantation is a suite of tools developed by the Kleinstein Lab as a complete analytical ecosytem for AIRR-seq data. The suite includes a variety of packages, both developed as part of Immancation or redistributed supporting tools. Immcantation currently includes Alakazam, Change-O, Dowser, pRESTO, SCOPer, SHazaM, and TIgGER.

References:

To cite the pRESTO software package in publications, please use:

Vander Heiden JA*, Yaari G*, Uduman M, Stern JNH, O’Connor KC, Hafler DA, Vigneault F, Kleinstein SH. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics 30, 1930-2 (2014). doi:10.1093/bioinformatics/btu138

To cite the Change-O, Alakazam, SHazaM and TIgGER software package in publications, please use:

Gupta NT*, Vander Heiden JA*, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 31, 3356-8 (2015). doi:10.1093/bioinformatics/btv359

Additional citations for specific methods within Alakazam, SHazaM, TIgGER, SCOper and Dowser may be determined using the citation() function within R.

• Immcantation Suite Documentation
• Alakazam Package Documentation
• Change-O Package Documentation
• Dowser Package Documentation
• pRESTO Package Documentation
• SCOPer Package Documentation
• SHazaM Package Documentation
• TIgGER Package Documentation

• Module Name: immcantation (see the modules page for more information)
• All commands and scripts for the included tools are available when loading the immcantation module.

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive --mem=10g
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job

[cn0135]$ cd /data/$USER/

[cn0135]$ module load immcantation

# Example Change-O command help
[cn0135]$ AlignRecords.py --help

# Example pRESTO command help
[cn0135]$ FilterSeq.py --help

# Show versions of all included tools
[cn0135]$ versions report
immcantation: 4.5.0
date: 2024.01.25

presto: 0.7.2
changeo: 1.3.0
alakazam: 1.3.0
shazam: 1.2.0
tigger: 1.1.0
scoper: 1.3.0
dowser: 2.1.0
...

[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.