Parallelized short read assembly of large genomes using de Bruijn graphs

Publikationstyp:
Zeitschriftenaufsatz
Metadaten:
Autoren
Sammlungen
  • metadata
ISSN
1471-2105
Zeitschrift
BMC bioinformatics
Schlüsselwörter
  • 600 Technik
  • 600 Technology (Applied sciences)
Sprache
eng
Paginierung
Art. 354
Datum der Veröffentlichung
2011
Herausgeber
BioMed Central
Herausgeber URL
http://dx.doi.org/10.1186/1471-2105-12-354
Datum der Datenerfassung
2020
Datum, an dem der Datensatz öffentlich gemacht wurde
2020
Zugang
Public
Titel
Parallelized short read assembly of large genomes using de Bruijn graphs
Ausgabe der Zeitschrift
12

Datenquelle: METADATA.UB

Andere Metadatenquellen:
Autoren
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000294558500001&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1186/1471-2105-12-354
Externe Identifier
  • Clarivate Analytics Document Solution ID: 815VQ
  • PubMed Identifier: 21867511
ISSN
1471-2105
Zeitschrift
BMC BIOINFORMATICS
Artikelnummer
ARTN 354
Datum der Veröffentlichung
2011
Status
Published
Titel
Parallelized short read assembly of large genomes using de Bruijn graphs
Sub types
  • Article
Ausgabe der Zeitschrift
12

Datenquelle: Web of Science (Lite)

Autoren
DOI
10.1186/1471-2105-12-354
eISSN
1471-2105
Ausgabe der Veröffentlichung
1
Zeitschrift
BMC Bioinformatics
Sprache
en
Artikelnummer
354
Online publication date
2011
Datum der Veröffentlichung
2011
Status
Published
Herausgeber
Springer Science and Business Media LLC
Herausgeber URL
http://dx.doi.org/10.1186/1471-2105-12-354
Datum der Datenerfassung
2019
Titel
Parallelized short read assembly of large genomes using de Bruijn graphs
Ausgabe der Zeitschrift
12

Datenquelle: Crossref

Abstract
<h4>Background</h4>Next-generation sequencing technologies have given rise to the explosive increase in DNA sequencing throughput, and have promoted the recent development of de novo short read assemblers. However, existing assemblers require high execution times and a large amount of compute resources to assemble large genomes from quantities of short reads.<h4>Results</h4>We present PASHA, a parallelized short read assembler using de Bruijn graphs, which takes advantage of hybrid computing architectures consisting of both shared-memory multi-core CPUs and distributed-memory compute clusters to gain efficiency and scalability. Evaluation using three small-scale real paired-end datasets shows that PASHA is able to produce more contiguous high-quality assemblies in shorter time compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. PASHA's scalability for large genome datasets is demonstrated with human genome assembly. Compared to ABySS, PASHA achieves competitive assembly quality with faster execution speed on the same compute resources, yielding an NG50 contig size of 503 with the longest correct contig size of 18,252, and an NG50 scaffold size of 2,294. Moreover, the human assembly is completed in about 21 hours with only modest compute resources.<h4>Conclusions</h4>Developing parallel assemblers for large genomes has been garnering significant research efforts due to the explosive size growth of high-throughput short read datasets. By employing hybrid parallelism consisting of multi-threading on multi-core CPUs and message passing on compute clusters, PASHA is able to assemble the human genome with high quality and in reasonable time using modest compute resources.
Addresses
  • School of Computer Engineering, Nanyang Technological University, Singapore. liuy0039@ntu.edu.sg
Autoren
DOI
10.1186/1471-2105-12-354
eISSN
1471-2105
Externe Identifier
  • PubMed Identifier: 21867511
  • PubMed Central ID: PMC3167803
Open access
true
ISSN
1471-2105
Zeitschrift
BMC bioinformatics
Schlüsselwörter
  • Humans
  • Bacteria
  • Computational Biology
  • Genome
  • Genome, Human
  • Software
  • High-Throughput Nucleotide Sequencing
Sprache
eng
Medium
Electronic
Online publication date
2011
Open access status
Open Access
Paginierung
354
Datum der Veröffentlichung
2011
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2011
Titel
Parallelized short read assembly of large genomes using de Bruijn graphs.
Sub types
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
12

Files

https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-354 https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21867511/pdf/?tool=EBI https://europepmc.org/articles/PMC3167803?pdf=render

Datenquelle: Europe PubMed Central

Abstract
BACKGROUND: Next-generation sequencing technologies have given rise to the explosive increase in DNA sequencing throughput, and have promoted the recent development of de novo short read assemblers. However, existing assemblers require high execution times and a large amount of compute resources to assemble large genomes from quantities of short reads. RESULTS: We present PASHA, a parallelized short read assembler using de Bruijn graphs, which takes advantage of hybrid computing architectures consisting of both shared-memory multi-core CPUs and distributed-memory compute clusters to gain efficiency and scalability. Evaluation using three small-scale real paired-end datasets shows that PASHA is able to produce more contiguous high-quality assemblies in shorter time compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. PASHA's scalability for large genome datasets is demonstrated with human genome assembly. Compared to ABySS, PASHA achieves competitive assembly quality with faster execution speed on the same compute resources, yielding an NG50 contig size of 503 with the longest correct contig size of 18,252, and an NG50 scaffold size of 2,294. Moreover, the human assembly is completed in about 21 hours with only modest compute resources. CONCLUSIONS: Developing parallel assemblers for large genomes has been garnering significant research efforts due to the explosive size growth of high-throughput short read datasets. By employing hybrid parallelism consisting of multi-threading on multi-core CPUs and message passing on compute clusters, PASHA is able to assemble the human genome with high quality and in reasonable time using modest compute resources.
Date of acceptance
2011
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/21867511
DOI
10.1186/1471-2105-12-354
eISSN
1471-2105
Externe Identifier
  • PubMed Central ID: PMC3167803
Zeitschrift
BMC Bioinformatics
Schlüsselwörter
  • Bacteria
  • Computational Biology
  • Genome
  • Genome, Human
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Software
Sprache
eng
Country
England
Paginierung
354
PII
1471-2105-12-354
Datum der Veröffentlichung
2011
Status
Published online
Datum, an dem der Datensatz öffentlich gemacht wurde
2011
Titel
Parallelized short read assembly of large genomes using de Bruijn graphs.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
12

Datenquelle: PubMed

Autoren
Zeitschrift
BMC Bioinform.
Paginierung
354 - 354
Datum der Veröffentlichung
2011
Titel
Parallelized short read assembly of large genomes using de Bruijn graphs.
Ausgabe der Zeitschrift
12

Datenquelle: DBLP

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