Notice

Colib’read project is now officially finished, but our efforts continue. Algorithmics and tools development are still ongoing.

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Computational pan-genomics: status, promises and challenges

• Authors:The Computational Pan-Genomics Consortium
• Details: Brief Bioinform (2016) bbw089.
• DOI: https://doi.org/10.1093/bib/bbw089

 

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

• Authors: Hélène Lopez-Maestre Lilia Brinza Camille Marchet Janice Kielbassa Sylvère Bastien Mathilde Boutigny David Monnin Adil El Filali Claudia Marcia Carareto Cristina Vieira Franck Picard Natacha Kremer Fabrice Vavre Marie-France Sagot Vincent Lacroix
• Details: Nucl Acids Res (2016) 44 (19): e148.
• DOI: https://doi.org/10.1093/nar/gkw655

A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics

• Authors: C. Marchet, A. Limasset, L. Bittner, P. Peterlongo
• Details: Prague Stringology Conference 2016, Praha, Czech Republic, August 29–31, 2016, Proceedings

Accurate self-correction of errors in long reads using de Bruijn graphs

• Authors: L Salmela, R Walve, E Rivals, E Ukkonen
• Details: Bioinformatics, 2016

Superstring Graph: a new approach for genome assembly

• Authors: B. Cazaux, G. Sacomoto, E. Rivals
• Details: Algorithmic Aspects in Information and Management, Bergamo, Italy, July 18-20, 2016, Lecture Notes in Computer Science (LNCS) series, Volume 9778, 39–52, 2016.

Read mapping on de Bruijn graphs

• Authors: A. Limasset, B. Cazaux, E. Rivals, P. Peterlongo
• Details: BMC Bioinformatics doi:10.1186/s12859-016-1103-9, 17:237, 2016.

A linear time algorithm for shortest cyclic cover of strings

• Authors: B. Cazaux, E. Rivals
• Details: Journal of Discrete Algorithms, http://dx.doi.org/10.1016/j.jda.2016.05.001, Volume 37, Pages 56–67, 2016.

Shortest DNA cyclic cover in compressed space

• Authors: B. Cazaux, R. Canovas, E. Rivals
• Details: Data Compression Conference (DCC), Snowbird, Utah, 27th March – 1 April, IEEE Computer Society Press, 536 – 545, 2016.
  DOI 10.1109/DCC.2016.79

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

• Authors: Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru and Pierre Peterlongo
• Details: GigaScience, doi:10.1186/s13742-015-0105-2, 2016.

SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

• Authors: Gilles Boutet, Susete Alves Carvalho, Matthieu Falque, Pierre Peterlongo, Emeline Lhuillier, Olivier Bouchez, Clément Lavaud, Marie-Laure Pilet-Nayel, Nathalie Rivière and Alain Baranger
• Details : BMC Genomics, doi:10.1186/s12864-016-2447-2, 2016.

 

 

Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.

• Authors: Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru and Guillaume Rizk
• Details: BMC Bioinformatics, doi:10.1186/s12859-015-0709-7, 16:288, 2015.
• Talk at WABI’2015: pdf

Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree

• Authors: Cazaux, Bastien, Lecroq, Thierry, & Rivals, Eric
• Details:In International Conference on Language and Automata Theory and Applications

YOC, a new strategy for pairwise alignment of collinear genomes

• Authors: R. Uricaru, C. Michotey, H. Chiapello, E. Rivals
• Details: BMC Bioinformatics doi:10.1186/s12859-015-0530-3, 16:111, 2015.

Reference-free detection of isolated SNPs.

• Full Text (PDF) – SUPPLEMENTARY DATA
• Authors: Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, Rayan Chikhi, Claire Lemaitre, Pierre Peterlongo
• Details: Nucleic Acids Research, (2014) doi: 10.1093/nar/gku1187

Amortized Õ (|V|)O~(|V|)-Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

• Authors: Rui Ferreira, Roberto Grossi, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot
• Details: In European Symposium on Algorithms. Springer Berlin Heidelberg.

Using cascading Bloom filters to improve the memory usage for de Brujin graph

• Authors: Salikhov, K., Sacomoto, G., & Kucherov, G.
• Details: Algorithms for Molecular Biology, 9, 2.

Navigating in a Sea of Repeats in RNA-seq without Drowning

• Authors: Sacomoto, G., Sinaimeri, B., Marchet, C., Miele, V., Sagot, M.-F., & Lacroix, V.
• Details: CoRR, abs/1406.1022.

Efficient Algorithms for de novo Assembly of Alternative Splicing Events from RNA-seq Data

• Authors: Sacomoto, G
• Details:Phd Thesis

MindTheGap : integrated detection and assembly of short and long insertions.

• Authors: Guillaume Rizk, Anaïs Gouin, Rayan Chikhi and Claire Lemaitre
• Details: Bioinformatics, 2014 30(24):3451-3457.
• Poster at ECCB’2014: pdf

LoRDEC: accurate and efficient long read error correction

• Authors: Leena Salmela, Eric Rivals
• Details: Bioinformatics, on line doi:10.1093/bioinformatics/btu538 August 26, 2014.

From Indexing Data Structures to de Bruijn Graphs

• Authors: Batien Cazaux, Thierry Lecroq, Eric Rivals
• Details: 25th Annual Symposium on Combinatorial Pattern Matching (CPM 2014), Moscow, LNCS 8486
• Presentation: here

Approximation of greedy algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings

• Authors: Bastien Cazaux, Eric Rivals
• Details: Prague Stringology Conference (PSC 2014), Prague, 2014.

Reverse Engineering of Compact Suffix Trees and Links: a Novel Algorithm

• Authors: Bastien Cazaux, Eric Rivals
• Details: Journal of Discrete Algorithms (2014) http://dx.doi.org/10.1016/j.jda.2014.07.002

Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome

• Authors: Susete Alves Carvalho, Raluca Uricaru, Jorge Duarte, Claire Lemaitre, Nathalie Rivière, Gilles Boutet, Alain Baranger and Pierre Peterlongo
• Details: ECCB 2014 poster, track Sequencing and sequence analysis for genomics

Commet: Comparing and combining multiple metagenomic datasets

• Autors : Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo
• Details :In Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference.

Mapping-free and Assembly-free Discovery of Inversion Breakpoints from Raw NGS Reads. 

• Authors: Claire Lemaitre, Liviu Ciortuz and Pierre Peterlongo.
• Details: Proceedings of AlCoB 2014, in Algorithms for Computational Biology, LNCS vol. 8542, pp. 119–130. (Springer link)
• Presentation: here

A Polynomial Delay Algorithm for the Enumeration of Bubbles with Length Constraints in Directed Graphs and Its Application to the Detection of Alternative Splicing in RNA-seq Data

• Autors : Sacomoto, G., Lacroix, V., & Sagot, M.-F.
• Details : Wabi 2013

CRAC: an integrated approach to the analysis of RNA-seq reads

• Autors : Nicolas Philippe, Mickael Salson, Thérèse Commes, Eric Rivals
• Details : Genome Biology, 14:R30, 2013.

Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data

• Autors : Niko Välimäki and Eric Rivals
• Details : 9th International Symposium on Bioinformatics Research and Applications ISBRA 2013, 20-22 May 2013 Lecture Notes in Bioinformatics (LNBI), Springer Verlag, Z. Cai et al. (Eds.), LNBI 7875, pp. 237 248, 2013.

Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms.

• Autors : Elsa Quillery, Olivier Quenez, Pierre Peterlongo, Olivier Plantard
• Details : Mol Ecol Resour, wiley, 2013,  <http://dx.doi.org/10.1111/1755-0998.12179>

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data 

• Autors : Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix
• Details : BMC Bioinformatics 2012, 13(Suppl 6):S5

Efficient bubble enumeration in directed graphs

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

 Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

• Autors :   Pierre Peterlongo and Rayan Chikhi
• Details : BMC Bioinformatics 2012, 13(1), 48. doi:10.1186/1471-2105-13-48.

 Space-efficient and exact de Bruijn graph representation based on a Bloom filter

• Autors :Rayan Chikhi and Guillaume Rizk
• Details : BMC Bioinformatics 2012, 13(Suppl 6):S5

Querying large read collections in main memory: a versatile data structure

• Autors : Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard
• Details : BMC Bioinformatics 2011

Identifying SNPs without a reference genome by comparing raw reads.

• Autors : Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix.
• Details : 17th International Symposium, SPIRE 2010, Los Cabos, Mexico, October 11-13, 2010, Proceedings