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CloudSPAdes : Assembly of synthetic long reads using de Bruijn graphs. / Tolstoganov, Ivan; Bankevich, Anton; Chen, Zhoutao; Pevzner, Pavel A.

в: Bioinformatics, Том 35, № 14, btz349, 15.07.2019, стр. i61-i70.

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

Harvard

Tolstoganov, I, Bankevich, A, Chen, Z & Pevzner, PA 2019, 'CloudSPAdes: Assembly of synthetic long reads using de Bruijn graphs', Bioinformatics, Том. 35, № 14, btz349, стр. i61-i70. https://doi.org/10.1093/bioinformatics/btz349

APA

Tolstoganov, I., Bankevich, A., Chen, Z., & Pevzner, P. A. (2019). CloudSPAdes: Assembly of synthetic long reads using de Bruijn graphs. Bioinformatics, 35(14), i61-i70. [btz349]. https://doi.org/10.1093/bioinformatics/btz349

Vancouver

Tolstoganov I, Bankevich A, Chen Z, Pevzner PA. CloudSPAdes: Assembly of synthetic long reads using de Bruijn graphs. Bioinformatics. 2019 Июль 15;35(14):i61-i70. btz349. https://doi.org/10.1093/bioinformatics/btz349

Author

Tolstoganov, Ivan ; Bankevich, Anton ; Chen, Zhoutao ; Pevzner, Pavel A. / CloudSPAdes : Assembly of synthetic long reads using de Bruijn graphs. в: Bioinformatics. 2019 ; Том 35, № 14. стр. i61-i70.

BibTeX

@article{cfd1642f97d1493c929d1559ff6cbf8f,
title = "CloudSPAdes: Assembly of synthetic long reads using de Bruijn graphs",
abstract = "Motivation: The recently developed barcoding-based synthetic long read (SLR) technologies have already found many applications in genome assembly and analysis. However, although some new barcoding protocols are emerging and the range of SLR applications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameters and are not easily extendable to new barcoding technologies and new applications such as metagenomics or hybrid assembly. Results: We describe the algorithmic challenge of the SLR assembly and present a cloudSPAdes algorithm for SLR assembly that is based on analyzing the de Bruijn graph of SLRs. We benchmarked cloudSPAdes across various barcoding technologies/applications and demonstrated that it improves on the state-of-the-art SLR assemblers in accuracy and speed.",
keywords = "conference paper, velocity, algorithm, Article, bioinformatics, ACCURATE, DNA EXTRACTION, GENOME",
author = "Ivan Tolstoganov and Anton Bankevich and Zhoutao Chen and Pevzner, {Pavel A.}",
year = "2019",
month = jul,
day = "15",
doi = "10.1093/bioinformatics/btz349",
language = "English",
volume = "35",
pages = "i61--i70",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "14",

}

RIS

TY - JOUR

T1 - CloudSPAdes

T2 - Assembly of synthetic long reads using de Bruijn graphs

AU - Tolstoganov, Ivan

AU - Bankevich, Anton

AU - Chen, Zhoutao

AU - Pevzner, Pavel A.

PY - 2019/7/15

Y1 - 2019/7/15

N2 - Motivation: The recently developed barcoding-based synthetic long read (SLR) technologies have already found many applications in genome assembly and analysis. However, although some new barcoding protocols are emerging and the range of SLR applications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameters and are not easily extendable to new barcoding technologies and new applications such as metagenomics or hybrid assembly. Results: We describe the algorithmic challenge of the SLR assembly and present a cloudSPAdes algorithm for SLR assembly that is based on analyzing the de Bruijn graph of SLRs. We benchmarked cloudSPAdes across various barcoding technologies/applications and demonstrated that it improves on the state-of-the-art SLR assemblers in accuracy and speed.

AB - Motivation: The recently developed barcoding-based synthetic long read (SLR) technologies have already found many applications in genome assembly and analysis. However, although some new barcoding protocols are emerging and the range of SLR applications is being expanded, the existing SLR assemblers are optimized for a narrow range of parameters and are not easily extendable to new barcoding technologies and new applications such as metagenomics or hybrid assembly. Results: We describe the algorithmic challenge of the SLR assembly and present a cloudSPAdes algorithm for SLR assembly that is based on analyzing the de Bruijn graph of SLRs. We benchmarked cloudSPAdes across various barcoding technologies/applications and demonstrated that it improves on the state-of-the-art SLR assemblers in accuracy and speed.

KW - conference paper

KW - velocity

KW - algorithm

KW - Article

KW - bioinformatics

KW - ACCURATE

KW - DNA EXTRACTION

KW - GENOME

UR - http://www.scopus.com/inward/record.url?scp=85068914178&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btz349

DO - 10.1093/bioinformatics/btz349

M3 - Article

C2 - 31510642

AN - SCOPUS:85068914178

VL - 35

SP - i61-i70

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 14

M1 - btz349

ER -

ID: 49523355