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

KisSplice Worklows and Applications to SNPs and AS

Helene Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvere Bastien, Mathilde Boutigny, David Monnin, Adil El Filali, Claudia Marcia Carareto, Cristina Vieira, Franck Picard, Natacha Kremer, Fabrice Vavre, Marie-France Sagot, Vincent Lacroix
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
Nucleic Acids Research, vol. 44 pp.1-13.

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto, Amandine Rey, Cyril Bourgeois, Didier Auboeuf, Vincent Lacroix
Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data
BiorXiV, September 2016

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>