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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: korobeynikov a. J Comput Biol. 2013 Oct;20(10):714-37. doi: 10.1089/cmb.2013.0084. J Comput Biol. 2013. PMID: 24093227 Free PMC article.
ExSPAnder: a universal repeat resolver for DNA fragment assembly.
Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner PA. Prjibelski AD, et al. Among authors: korobeynikov a. Bioinformatics. 2014 Jun 15;30(12):i293-301. doi: 10.1093/bioinformatics/btu266. Bioinformatics. 2014. PMID: 24931996 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. Among authors: korobeynikov a. Bioinformatics. 2016 Apr 1;32(7):1009-15. doi: 10.1093/bioinformatics/btv688. Epub 2015 Nov 20. Bioinformatics. 2016. PMID: 26589280 Free PMC article.
metaSPAdes: a new versatile metagenomic assembler.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. Nurk S, et al. Among authors: korobeynikov a. Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15. Genome Res. 2017. PMID: 28298430 Free PMC article.
Using SPAdes De Novo Assembler.
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Prjibelski A, et al. Among authors: korobeynikov a. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102. Curr Protoc Bioinformatics. 2020. PMID: 32559359
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: korobeynikov a. 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.
45 results