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plasmidSPAdes: assembling plasmids from whole genome sequencing data.
Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA. Antipov D, et al. Bioinformatics. 2016 Nov 15;32(22):3380-3387. doi: 10.1093/bioinformatics/btw493. Epub 2016 Jul 27. Bioinformatics. 2016. PMID: 27466620
AVAILABILITY AND IMPLEMENTATION: plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online....
AVAILABILITY AND IMPLEMENTATION: plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.an …
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.
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.
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.
Metaviral SPAdes: assembly of viruses from metagenomic data.
Antipov D, Raiko M, Lapidus A, Pevzner PA. Antipov D, et al. Bioinformatics. 2020 Aug 15;36(14):4126-4129. doi: 10.1093/bioinformatics/btaa490. Bioinformatics. 2020. PMID: 32413137
AVAILABILITY AND IMPLEMENTATION: Metaviral SPAdes includes ViralAssembly, ViralVerify and ViralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/abla …
AVAILABILITY AND IMPLEMENTATION: Metaviral SPAdes includes ViralAssembly, ViralVerify and ViralComplete modules that are available as standa …
22 results