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)