Immcantation on Biowulf
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.


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.

Important Notes
Submitting an interactive job

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]$ --help

# Example pRESTO command help
[cn0135]$ --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salloc.exe: Job allocation 789523 has been revoked.