List of analysis pipelines

[ematsen]

This is a growing list of pipelines for analyzing immune repertoire data. Please post a reply if you know of something that is not here.

• Automation (Michaeli et al. 2012)
• Change-O (Gupta et al. 2015)
• IGGalaxy (Moorhouse et al 2014 )
• ImmunediveRsity (Cortina-Ceballos et al. 2015)
• migmap : postprocessor of IgBLAST output
• pRESTO (Vander Heiden et al 2014)
• sciReptor (Imkeller et al 2016); especially for single-cell data
• SONAR (Schramm et al 2016)
• tcR (Narazov et al. 2015)
• TRIgS (Lees and Shepherd 2015)
• VDJtools (Shugay et al. 2015)
• VDJPipe (Christley et al. 2017)

[ematsen]

Presto just got some fancy new documentation at Read The Docs: http://presto.readthedocs.org/en/latest/

[javh]

Here’s another list of repertoire tools:
http://omictools.com/rep-seq-category

[chris.cottrell]

VDJPipe Christly et al. 2017

[ematsen]

Added. I’ve turned it into a wiki so anyone can contribute.

Thanks!