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HybridSPAdes : An algorithm for hybrid assembly of short and long reads. / Antipov, Dmitry; Korobeynikov, Anton; McLean, Jeffrey S.; Pevzner, Pavel A.

In: Bioinformatics, Vol. 32, No. 7, 01.04.2016, p. 1009-1015.

Research output: Contribution to journal › Article › peer-review

Harvard

Antipov, D, Korobeynikov, A, McLean, JS & Pevzner, PA 2016, 'HybridSPAdes: An algorithm for hybrid assembly of short and long reads', Bioinformatics, vol. 32, no. 7, pp. 1009-1015. https://doi.org/10.1093/bioinformatics/btv688, https://doi.org/10.1093/bioinformatics/btv688

APA

Antipov, D., Korobeynikov, A., McLean, J. S., & Pevzner, P. A. (2016). HybridSPAdes: An algorithm for hybrid assembly of short and long reads. Bioinformatics, 32(7), 1009-1015. https://doi.org/10.1093/bioinformatics/btv688, https://doi.org/10.1093/bioinformatics/btv688

Vancouver

Antipov D, Korobeynikov A, McLean JS, Pevzner PA. HybridSPAdes: An algorithm for hybrid assembly of short and long reads. Bioinformatics. 2016 Apr 1;32(7):1009-1015. https://doi.org/10.1093/bioinformatics/btv688, https://doi.org/10.1093/bioinformatics/btv688

Author

Antipov, Dmitry ; Korobeynikov, Anton ; McLean, Jeffrey S. ; Pevzner, Pavel A. / HybridSPAdes : An algorithm for hybrid assembly of short and long reads. In: Bioinformatics. 2016 ; Vol. 32, No. 7. pp. 1009-1015.

BibTeX

@article{c7a42d5005134e219060b46ba5bd26dd,
title = "HybridSPAdes: An algorithm for hybrid assembly of short and long reads",
abstract = "Motivation: Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost. Results: We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads. 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.",
author = "Dmitry Antipov and Anton Korobeynikov and McLean, {Jeffrey S.} and Pevzner, {Pavel A.}",
note = "Publisher Copyright: {\textcopyright} 2015 The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.",
year = "2016",
month = apr,
day = "1",
doi = "10.1093/bioinformatics/btv688",
language = "English",
volume = "32",
pages = "1009--1015",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "7",

}

RIS

TY - JOUR

T1 - HybridSPAdes

T2 - An algorithm for hybrid assembly of short and long reads

AU - Antipov, Dmitry

AU - Korobeynikov, Anton

AU - McLean, Jeffrey S.

AU - Pevzner, Pavel A.

N1 - Publisher Copyright: © 2015 The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

PY - 2016/4/1

Y1 - 2016/4/1

N2 - Motivation: Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost. Results: We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads. 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.

AB - Motivation: Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost. Results: We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads. 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.

UR - http://www.scopus.com/inward/record.url?scp=84964474556&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btv688

DO - 10.1093/bioinformatics/btv688

M3 - Article

C2 - 26589280

VL - 32

SP - 1009

EP - 1015

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 7

ER -

ID: 7954363