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Critical Assessment of Metagenome Interpretation: the second round of challenges.
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Meyer F, et al. Among authors: lemaitre c. Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8. Nat Methods. 2022. PMID: 35396482 Free PMC article.
Compareads: comparing huge metagenomic experiments.
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P. Maillet N, et al. Among authors: lemaitre c. BMC Bioinformatics. 2012;13 Suppl 19(Suppl 19):S10. doi: 10.1186/1471-2105-13-S19-S10. Epub 2012 Dec 19. BMC Bioinformatics. 2012. PMID: 23282463 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: lemaitre c. Bioinformatics. 2014 Oct 15;30(20):2959-61. doi: 10.1093/bioinformatics/btu406. Epub 2014 Jul 1. Bioinformatics. 2014. PMID: 24990603 Free PMC article.
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: lemaitre c. 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.
Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.
Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P. Le Bras Y, et al. Among authors: lemaitre c. Gigascience. 2016 Feb 11;5:9. doi: 10.1186/s13742-015-0105-2. eCollection 2016. Gigascience. 2016. PMID: 26870323 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: lemaitre c. 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.
SVJedi: genotyping structural variations with long reads.
Lecompte L, Peterlongo P, Lavenier D, Lemaitre C. Lecompte L, et al. Among authors: lemaitre c. Bioinformatics. 2020 Nov 1;36(17):4568-4575. doi: 10.1093/bioinformatics/btaa527. Bioinformatics. 2020. PMID: 32437523
109 results