ExSPAnder: A universal repeat resolver for DNA fragment assembly

Andrey D. Prjibelski; Irina Vasilinetc; Anton Bankevich; Alexey Gurevich; Tatiana Krivosheeva; Sergey Nurk; Son Pham; Anton Korobeynikov; Alla Lapidus; Pavel A. Pevzner

doi:10.1093/bioinformatics/btu266

ExSPAnder: A universal repeat resolver for DNA fragment assembly

Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus, Pavel A. Pevzner

Computer Science and Engineering

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

Abstract

Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.

Original language	English (US)
Pages (from-to)	I293-I301
Journal	Bioinformatics
Volume	30
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/btu266
State	Published - Jun 15 2014

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btu266

Cite this

@article{9a0873c3210c49f4a11ffba6185143b4,

title = "ExSPAnder: A universal repeat resolver for DNA fragment assembly",

abstract = "Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.",

author = "Prjibelski, {Andrey D.} and Irina Vasilinetc and Anton Bankevich and Alexey Gurevich and Tatiana Krivosheeva and Sergey Nurk and Son Pham and Anton Korobeynikov and Alla Lapidus and Pevzner, {Pavel A.}",

note = "Funding Information: Funding: This work was supported by the Government of the Russian Federation [grant numbers 11.G34.31.0018, 11.G34.31.0068]; the National Institutes of Health [3P41RR024851-02S1]; and the Russian Fund for Basic Research [12-01-00747-a to A.K.].",

year = "2014",

month = jun,

day = "15",

doi = "10.1093/bioinformatics/btu266",

language = "English (US)",

volume = "30",

pages = "I293--I301",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "12",

}

TY - JOUR

T1 - ExSPAnder

T2 - A universal repeat resolver for DNA fragment assembly

AU - Prjibelski, Andrey D.

AU - Vasilinetc, Irina

AU - Bankevich, Anton

AU - Gurevich, Alexey

AU - Krivosheeva, Tatiana

AU - Nurk, Sergey

AU - Pham, Son

AU - Korobeynikov, Anton

AU - Lapidus, Alla

AU - Pevzner, Pavel A.

N1 - Funding Information: Funding: This work was supported by the Government of the Russian Federation [grant numbers 11.G34.31.0018, 11.G34.31.0068]; the National Institutes of Health [3P41RR024851-02S1]; and the Russian Fund for Basic Research [12-01-00747-a to A.K.].

PY - 2014/6/15

Y1 - 2014/6/15

N2 - Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.

AB - Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.

UR - http://www.scopus.com/inward/record.url?scp=84902509478&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84902509478&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btu266

DO - 10.1093/bioinformatics/btu266

M3 - Article

C2 - 24931996

AN - SCOPUS:84902509478

SN - 1367-4803

VL - 30

SP - I293-I301

JO - Bioinformatics

JF - Bioinformatics

IS - 12

ER -

ExSPAnder: A universal repeat resolver for DNA fragment assembly

Abstract

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this