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Using SPAdes De Novo Assembler. / Prjibelski , Andrey ; Antipov, Dmitry ; Meleshko , Dmitry ; Lapidus, Alla ; Korobeynikov, Anton .

в: Current Protocols in Bioinformatics, Том 70, № 1, e102, 19.06.2020.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

Harvard

Prjibelski , A, Antipov, D, Meleshko , D, Lapidus, A & Korobeynikov, A 2020, 'Using SPAdes De Novo Assembler', Current Protocols in Bioinformatics, Том. 70, № 1, e102. https://doi.org/10.1002/cpbi.102

APA

Prjibelski , A., Antipov, D., Meleshko , D., Lapidus, A., & Korobeynikov, A. (2020). Using SPAdes De Novo Assembler. Current Protocols in Bioinformatics, 70(1), [e102]. https://doi.org/10.1002/cpbi.102

Vancouver

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Current Protocols in Bioinformatics. 2020 Июнь 19;70(1). e102. https://doi.org/10.1002/cpbi.102

Author

Prjibelski , Andrey ; Antipov, Dmitry ; Meleshko , Dmitry ; Lapidus, Alla ; Korobeynikov, Anton . / Using SPAdes De Novo Assembler. в: Current Protocols in Bioinformatics. 2020 ; Том 70, № 1.

BibTeX

@article{25bb1b7b51434ed7a9c709a9b78dfe46,
title = "Using SPAdes De Novo Assembler",
abstract = "SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. ",
keywords = "de novo assembly, genome assembly, plasmids, metagenomes, transcriptome, biosynthetic gene clusters, de novo assembly, genome assembly, metagenomes, plasmids, transcriptome",
author = "Andrey Prjibelski and Dmitry Antipov and Dmitry Meleshko and Alla Lapidus and Anton Korobeynikov",
note = "Publisher Copyright: {\textcopyright} 2020 Wiley Periodicals LLC",
year = "2020",
month = jun,
day = "19",
doi = "10.1002/cpbi.102",
language = "English",
volume = "70",
journal = "Current Protocols in Bioinformatics",
issn = "1934-3396",
publisher = "Wiley-Blackwell",
number = "1",

}

RIS

TY - JOUR

T1 - Using SPAdes De Novo Assembler

AU - Prjibelski , Andrey

AU - Antipov, Dmitry

AU - Meleshko , Dmitry

AU - Lapidus, Alla

AU - Korobeynikov, Anton

N1 - Publisher Copyright: © 2020 Wiley Periodicals LLC

PY - 2020/6/19

Y1 - 2020/6/19

N2 - SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly.

AB - SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly.

KW - de novo assembly

KW - genome assembly

KW - plasmids

KW - metagenomes

KW - transcriptome

KW - biosynthetic gene clusters

KW - de novo assembly

KW - genome assembly

KW - metagenomes

KW - plasmids

KW - transcriptome

UR - https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.102

UR - http://www.scopus.com/inward/record.url?scp=85086752343&partnerID=8YFLogxK

U2 - 10.1002/cpbi.102

DO - 10.1002/cpbi.102

M3 - Article

VL - 70

JO - Current Protocols in Bioinformatics

JF - Current Protocols in Bioinformatics

SN - 1934-3396

IS - 1

M1 - e102

ER -

ID: 58463772