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Reference-free detection of isolated SNPs.
Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O, Chikhi R, Lemaitre C, Peterlongo P. Uricaru R, et al. Among authors: rizk g. Nucleic Acids Res. 2015 Jan;43(2):e11. doi: 10.1093/nar/gku1187. Epub 2014 Nov 17. Nucleic Acids Res. 2015. PMID: 25404127 Free PMC article.
GATB: Genome Assembly & Analysis Tool Box.
Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D. Drezen E, et al. Among authors: rizk g. Bioinformatics. 2014 Oct 15;30(20):2959-61. doi: 10.1093/bioinformatics/btu406. Epub 2014 Jul 1. Bioinformatics. 2014. PMID: 24990603 Free PMC article.
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Sczyrba A, et al. Among authors: rizk g. Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2. Nat Methods. 2017. PMID: 28967888 Free PMC article.
GASSST: global alignment short sequence search tool.
Rizk G, Lavenier D. Rizk G, et al. Bioinformatics. 2010 Oct 15;26(20):2534-40. doi: 10.1093/bioinformatics/btq485. Epub 2010 Aug 24. Bioinformatics. 2010. PMID: 20739310 Free PMC article.
DSK: k-mer counting with very low memory usage.
Rizk G, Lavenier D, Chikhi R. Rizk G, et al. Bioinformatics. 2013 Mar 1;29(5):652-3. doi: 10.1093/bioinformatics/btt020. Epub 2013 Jan 16. Bioinformatics. 2013. PMID: 23325618
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.
Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PAJ, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T. Wucher V, et al. Among authors: rizk g. Nucleic Acids Res. 2017 May 5;45(8):e57. doi: 10.1093/nar/gkw1306. Nucleic Acids Res. 2017. PMID: 28053114 Free PMC article.
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