A list of software that can perform V(D)J mapping for RNA-Seq, single-cell RNA sequencing, etc and extract complex rearrangements typical for lymphomas.
This is a wiki page. Please edit and add software you know about. However, note that this is not the place for closed-source commercial software vendors to advertise their products.
RNA-Seq data:
- V’DJer (Mose et al. 2016)
- MiXCR (Bolotin et al. 2015)
- TRUST (Li et al. 2016)
- ImReP(Mangul et al. 2016)
Single-cell RNA sequencing data:
- sciReptor (Imkeller et al. 2016)
- TraCeR (Stubbington et al. 2016)
- MiXCR (Bolotin et al. 2015)
- VDJPuzzle(Eltahla et al. 2016)
Complex rearrangements:
- vidjil (Giraud et al. 2014) : works with Dh/Jh, Dδ2/Dδ3, KDE-Intron, etc rearrangements