Applications Supporting the Rearrangement SchemaΒΆ

The following list of software tools and databases support the TSV format of v1.2 of the AIRR Rearrangement schema.

Software

Version

Support

Reference

AIRR Python Library

1.2

Input, output and validation

Vander Heiden et al. Front Immunol, 2018.

AIRR R Library

1.2

Input, output and validation

Vander Heiden et al. Front Immunol, 2018.

Alakazam

1.0.1

Input and output

Gupta & Vander Heiden et al. Bioinformatics, 2015.

Cell Ranger

4.0

Output

10x Genomics, Inc. Pleasanton, CA USA.

Change-O

0.4.2

Input, output and conversion

Gupta & Vander Heiden et al. Bioinformatics, 2015.

Decombinator

4.0.1

Output

Oakes et al. Front Immunol, 2017.

IMGT/HighV-QUEST

1.7.0

Output

Alamyar et al. Methods Mol Biol, 2012.

IMGT/V-QUEST

3.5.16

Output

Giudicelli et al. Cold Spring Harb Protoc, 2011.

IgBLAST

1.11

Output

Ye et al. Nucleic Acids Res, 2013.

immunarch

0.6.5

Input

ImmunoMind Team. 2019

ImmuneDB

0.24.0

Output

Rosenfeld et al. Front Immunol, 2018.

immuneSIM

0.8.7

Output

Weber et al. Bioinformatics, 2020.

iReceptor

3.0

Input and output

Corrie et al. Immunol Rev, 2018.

MiXCR

3.0.14

Output

Bolotin et al. Nat Methods, 2015.

RAbHIT

0.1.5

Input and output

Gidoni et al. Nat Commun, 2019.

scirpy

0.7

Input and output

Sturm et al. Bioinformatics, 2020.

SCOPer

1.0.1

Input and output

Nouri & Kleinstein. Bioinformatics, 2018.

SHazaM

1.0.0

Input and output

Gupta & Vander Heiden et al. Bioinformatics, 2015.

SONAR

3

Output

Schramm et al. Front Immunol, 2016.

sumrep

1.0

Input

Olson et al. Front Immunol, 2019.

TIgGER

1.0.0

Input and output

Gadala-Maria et al. PNAS, 2015.

TRIgS

2

Input

Lees & Shepherd. J Immunol Res, 2015.

VDJServer

1.2.0

Input and output

Christley et al. Front Immunol, 2018

Vidjil-algo

2018.1

Output

Giraud et al. BMC Genomics, 2014.

Vidjil Web Platform

TBD

Input and conversion

Duez et al. PLoS ONE, 2016.

IGoR

TBD

Input and output

Marcou et al. Nat Commun, 2018.

OLGA

TBD

Input and output

Sethna et al. Bioinformatics, 2019.

Partis

TBD

Output

Ralph & Matsen. PLoS Comput Biol, 2016.