Notice
Colib’read project is now officially finished, but our efforts continue. Algorithmics and tools development are still ongoing.
Notice
Colib’read project is now officially finished, but our efforts continue. Algorithmics and tools development are still ongoing.2016
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.
2015
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.
2014
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
Efficiently listing bounded length st-paths
- Authors: R Rizzi, G Sacomoto, MF Sagot
- Details:International Workshop on Combinatorial Algorithms
Integrating a new visualization tool in Galaxy
- Authors: Alexan Andrieux, Pierre Peterlongo, Yvan Le Bras, Cyril Moujaud, Charles Deltel
- Details: Galaxy Community Conference 2014. https://wiki.galaxyproject.org/Events/GCC2014/Abstracts/Posters
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
2013 -These publications are related to the topic, but were not produced under the project
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>
2012 – These publications are related to the topic, but were not produced under the project
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
2011
Querying large read collections in main memory: a versatile data structure
- Autors : Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard
- Details : BMC Bioinformatics 2011
2010
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