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Publications
GATB-CORE
E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier. (2014)GATB: Genome Assembly & Analysis Tool Box .Bioinformatics, 30(20):2959-2961. / BioIT 2014 poster
R. Chikhi, G. Rizk. (2013)Space-efficient and exact de Bruijn graph representation based on a Bloom filter .Algorithms for Molecular Biology 2013, 8:22
K.l Salikhov, G. Sacomoto, G. Kucherov. (2013)Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs Algorithms in Bioinformatics, Lecture Notes in Computer Science, Volume 8126, 2013, pp 364-376
Tools relying on GATB-CORE made by the GATB team
[BCALM 2 ] Chikhi R., Limasset A., Medvedev P. (2016)Compacting de Bruijn graphs from sequencing data quickly and in low memory .Bioinformatics. 32(12):i201-i208
[DiscoSNP ] Uricaru R., Rizk G., Lacroix V., Quillery E., Plantard O., Chikhi R., Lemaitre., Perterlongo P. (2015)Reference-free detection of isolated SNPs .Nucl. Acids Res. 43(2):e11
[LEON ] G. Benoit, C. Lemaitre, D. Lavenier, E. Drezen, T. Dayris, R. Uricaru, G. Rizk. (2015)Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph .BMC Bioinformatics, 2015, 16:288
[MindTheGap ] G. Rizk, A. Goin, R. Chikhi, C. Lemaitre. (2014)MindTheGap : integrated detection and assembly of short and long insertions .Bioinformatics, 30(24):3451-3457
[DSK ] G. Rizk, D. Lavenier, R. Chikhi. (2013)DSK: k-mer counting with very low memory usage .Bioinformatics, 29(5):652-3
[SRC ] Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo (2016)
[Simka ] Benoit G, Peterlongo P, Mariadassou M, Drezen E, Schbath S, Lavenier D, Lemaitre C. (2016)Multiple comparative metagenomics using multiset k-mer counting . PeerJ Computer Science 2:e94
Tools relying on GATB-CORE made by other research teams
[pySeer ] John A Lees, Marco Galardini, Stephen D Bentley, Jeffrey N Weiser, Jukka Corander (2018) pyseer: a comprehensive tool for microbial pangenome-wide association studies. Bioinformatics.
[DBGWAS ] M. Jaillard, L. Lima, M.Tournoud, P. Mahé, A. van Belkum, V. Lacroix, L. Jacob (2018)
[ORNA ] D. Durai, M. Schulz. (2017)In-Silico Read Normalization Using Set Multi-Cover Optimization .
[LoRMA ] L. Salmela, R. Walve, E. Rivals, and E. Ukkonen. (2016)Accurate self-correction of errors in long reads using de Bruijn graphs .
[LoRDEC ] L. Salmela, E. Rivals. (2014)LoRDEC: accurate and efficient long read error correction .Bioinformatics, 30 (24): 3506-3514, 2014.
[Gap2Seq ] L. Salmela, K. Sahlin, V. Mäkinen, and A.I. Tomescu. (2015)Gap Filling as Exact Path Length Problem .RECOMB 2015, Lecture Notes in Bioinformatics 9029, Springer 2015, 281–292.
[MixTaR] G. Fertin, G. Jean, A. Radulescu and I. Rusu. (2015)Hybrid de novo tandem repeat detection using short and long reads .BMC Medical Genomics 2015, 8(Suppl 3):S5
[Kover ] Drouin, A., Giguère, S., Déraspe, M., Marchand, M., Tyers, M., Loo, V. G., Bourgault, A. M., Laviolette, F. & Corbeil, J. (2016).Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons.
Publications using results made with GATB-CORE/GATB-TOOLS
Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu (2015)Genome-Scale Algorithm Design
D. Travisany et al (2017)Predicting the Metagenomics Content with Multiple CART Trees Mathematical Models in Biology
V. Wucher, F. Legeai, B. Hédan, G. Rizk, et al (2017)FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome Nucleic Acids Research
C. Marchet, A. Limasset, L. Bittner and P. Peterlongo. (2016)A resource-frugal probabilistic dictionary and applications in (meta)genomics .Prageu Stringology Conference , Aug 2016, Prague, Czech Republic
G. Boutet et al (2016)SNP discovery and genetic mapping in pea. BMC Genomics , 2016
H. Li. (2015)Correcting Illumina sequencing errors for human data .arXiv preprint arXiv:1502.03744.
D. Laehnemann, A. Borkhardt and A.C. McHardy. (2015)Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction .Briefings in Bioinformatics, bbv029.
S. Thongthawee and H. Volkaert. (2014)Analysis of teak (Tectona grandis) genome and its diversity .26th annual Meeting of the Thai Society for Biotechnology and intl. conf.
E. Quillery, O. Quenez, P. Peterlongo and O. Plantard (2013)Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms .Molecular Ecology Resources, 14(2):393–400
G. Collet, G. Rizk, R. Chikhi, D. Lavenier. (2013)Minia on Raspberry Pi, assembling a 100 Mbp genome on a Credit Card Sized Computer .Poster at the JOBIM conference, 2013 Jul 1-4 (Toulouse, France) . Best poster award.
Studies, Challenges, …
GATB-Tools have been used during the 1st CAMI Challenge (Critical Assessment of Metagenome Interpretation ) – Dataset 2 – CAMI_medium.Follow this link to read results evaluation.
