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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: antipov d. 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.
Using SPAdes De Novo Assembler.
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Prjibelski A, et al. Among authors: antipov d. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102. Curr Protoc Bioinformatics. 2020. PMID: 32559359
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. Bankevich A, et al. Among authors: antipov d. J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16. J Comput Biol. 2012. PMID: 22506599 Free PMC article.
hybridSPAdes: an algorithm for hybrid assembly of short and long reads.
Antipov D, Korobeynikov A, McLean JS, Pevzner PA. Antipov D, et al. Bioinformatics. 2016 Apr 1;32(7):1009-15. doi: 10.1093/bioinformatics/btv688. Epub 2015 Nov 20. Bioinformatics. 2016. PMID: 26589280 Free PMC article.
AVAILABILITY AND IMPLEMENTATION: hybridSPAdes is implemented in C++ as a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades CONTACT: d.antipov@spbu.ru SUPPLEMENTARY INFORMATION: supplementary data are available at Bioinform …
AVAILABILITY AND IMPLEMENTATION: hybridSPAdes is implemented in C++ as a part of SPAdes genome assembler and is publicly available at http:/ …
Versatile genome assembly evaluation with QUAST-LG.
Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A. Mikheenko A, et al. Among authors: antipov d. Bioinformatics. 2018 Jul 1;34(13):i142-i150. doi: 10.1093/bioinformatics/bty266. Bioinformatics. 2018. PMID: 29949969 Free PMC article.
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.
Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. Nurk S, et al. Among authors: antipov d. J Comput Biol. 2013 Oct;20(10):714-37. doi: 10.1089/cmb.2013.0084. J Comput Biol. 2013. PMID: 24093227 Free PMC article.
21 results