KisSplice

A local transcriptome assembler for SNPs, indels and AS events

First KisSplice publication:

Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix, KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinformatics 2012, 13(Suppl 6):S5

Improvements of methods in KisSplice:

Etienne Birmele, Pierluigi Crescenzi, Rui Ferreira, Roberto Grossi, Vincent Lacroix, Andrea Marino, Nadia Pisanti, Gustavo AT Sacomoto and Marie-France Sagot, Efficient bubble enumeration in directed graphs.
Proceedings of 19th Conference on String Processing and Information Retrieval (SPIRE) 2012, Springer LNCS 7608, pages 118-129, 2012.

Gustavo AT Sacomoto, Vincent Lacroix and Marie-France Sagot A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs, Algorithms for Molecular Biology, 10:20, 2015

Gustavo AT Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix Navigating in a sea of repeats in RNA-seq without drowning Proceedings of 14th Workshop on Algorithms in Bioinformatics (WABI) 2014, Springer LNCS 8701, pages 82-96, 2014

Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot and Vincent Lacroix. Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. Algorithms for Molecular Biology, 2017, 12 (1), pp.2. <10.1186/s13015-017-0091-2>

Application of KisSplice's workflow for SNPs

Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, Filali A E, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V SNP calling from RNA-seq data without a reference genome: identification quantification differential analysis and impact on the protein sequence, Nucleic acids research, DOI