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)
  A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics.
  Stringology 2016: 85-97
• [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)
  A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between kmers and genetic events. Plos Genet.
• [ORNA] D. Durai, M. Schulz. (2017)
  In-Silico Read Normalization Using Set Multi-Cover Optimization.
  bioRxiv.
• [LoRMA] L. Salmela, R. Walve, E. Rivals, and E. Ukkonen. (2016)
  Accurate self-correction of errors in long reads using de Bruijn graphs.
  Bioinformatics, Advanced access. 10.1093/bioinformatics/btw321.
• [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.
  BMC Genomics, 17(1), 754

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.