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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. 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.
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: bankevich 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: bankevich a. Bioinformatics. 2014 Jun 15;30(12):i293-301. doi: 10.1093/bioinformatics/btu266. Bioinformatics. 2014. PMID: 24931996 Free PMC article.
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
Safonova Y, Bankevich A, Pevzner PA. Safonova Y, et al. Among authors: bankevich a. J Comput Biol. 2015 Jun;22(6):528-45. doi: 10.1089/cmb.2014.0153. Epub 2015 Mar 3. J Comput Biol. 2015. PMID: 25734602 Free PMC article.
TruSPAdes: barcode assembly of TruSeq synthetic long reads.
Bankevich A, Pevzner PA. Bankevich A, et al. Nat Methods. 2016 Mar;13(3):248-50. doi: 10.1038/nmeth.3737. Epub 2016 Feb 1. Nat Methods. 2016. PMID: 26828418
Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.
Kim S, Cho YS, Kim HM, Chung O, Kim H, Jho S, Seomun H, Kim J, Bang WY, Kim C, An J, Bae CH, Bhak Y, Jeon S, Yoon H, Kim Y, Jun J, Lee H, Cho S, Uphyrkina O, Kostyria A, Goodrich J, Miquelle D, Roelke M, Lewis J, Yurchenko A, Bankevich A, Cho J, Lee S, Edwards JS, Weber JA, Cook J, Kim S, Lee H, Manica A, Lee I, O'Brien SJ, Bhak J, Yeo JH. Kim S, et al. Among authors: bankevich a. Genome Biol. 2016 Oct 11;17(1):211. doi: 10.1186/s13059-016-1071-4. Genome Biol. 2016. PMID: 27802837 Free PMC article.
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.
Tolstoganov I, Bankevich A, Chen Z, Pevzner PA. Tolstoganov I, et al. Among authors: bankevich a. Bioinformatics. 2019 Jul 15;35(14):i61-i70. doi: 10.1093/bioinformatics/btz349. Bioinformatics. 2019. PMID: 31510642 Free PMC article.
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.
Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. Sanders JG, et al. Among authors: bankevich a. Genome Biol. 2019 Oct 31;20(1):226. doi: 10.1186/s13059-019-1834-9. Genome Biol. 2019. PMID: 31672156 Free PMC article.
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