CUSHAW3 : sensitive and accurate base-space and color-space short-read alignment with hybrid seeding

Publication type:
Journal article
Metadata:
Autoren
Sammlungen
  • metadata
ISSN
1932-6203
Ausgabe der Veröffentlichung
1
Zeitschrift
PLoS one
Schlüsselwörter
  • 004 Informatik
  • 004 Data processing
Sprache
eng
Paginierung
e86869
Datum der Veröffentlichung
2014
Herausgeber
PLoS
Herausgeber URL
http://dx.doi.org/10.1371/journal.pone.0086869
Datum der Datenerfassung
2020
Datum, an dem der Datensatz öffentlich gemacht wurde
2020
Zugang
Public
Titel
CUSHAW3 : sensitive and accurate base-space and color-space short-read alignment with hybrid seeding
Ausgabe der Zeitschrift
9

Data source: METADATA.UB

Other metadata sources:
Autoren
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000330283100227&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1371/journal.pone.0086869
Externe Identifier
  • Clarivate Analytics Document Solution ID: 297VL
  • PubMed Identifier: 24466273
ISSN
1932-6203
Ausgabe der Veröffentlichung
1
Zeitschrift
PLOS ONE
Artikelnummer
ARTN e86869
Datum der Veröffentlichung
2014
Status
Published
Titel
CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
Sub types
  • Article
Ausgabe der Zeitschrift
9

Data source: Web of Science (Lite)

Autoren
DOI
10.1371/journal.pone.0086869
Editoren
  • Oliver Hofmann
eISSN
1932-6203
Ausgabe der Veröffentlichung
1
Zeitschrift
PLoS ONE
Sprache
en
Online publication date
2014
Paginierung
e86869 - e86869
Status
Published online
Herausgeber
Public Library of Science (PLoS)
Herausgeber URL
http://dx.doi.org/10.1371/journal.pone.0086869
Datum der Datenerfassung
2020
Titel
CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
Ausgabe der Zeitschrift
9

Data source: Crossref

Abstract
The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorporates three different seed types, i.e. maximal exact match seeds, exact-match k-mer seeds and variable-length seeds, into the alignment pipeline. Furthermore, three techniques: weighted seed-pairing heuristic, paired-end alignment pair ranking and read mate rescuing have been conceived to facilitate accurate paired-end alignment. For base-space alignment, we have compared CUSHAW3 to Novoalign, CUSHAW2, BWA-MEM, Bowtie2 and GEM, by aligning both simulated and real reads to the human genome. The results show that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novoalign for short-reads with high error rates. For color-space alignment, CUSHAW3 is consistently one of the best aligners compared to SHRiMP2 and BFAST. The source code of CUSHAW3 and all simulated data are available at http://cushaw3.sourceforge.net.
Addresses
  • Institut für Informatik, Johannes Gutenberg Universität Mainz, Mainz, Germany.
Autoren
DOI
10.1371/journal.pone.0086869
eISSN
1932-6203
Externe Identifier
  • PubMed Identifier: 24466273
  • PubMed Central ID: PMC3899341
Open access
true
ISSN
1932-6203
Ausgabe der Veröffentlichung
1
Zeitschrift
PloS one
Schlüsselwörter
  • Sequence Alignment
  • Computational Biology
  • Base Sequence
  • Computer Simulation
  • Software
  • High-Throughput Nucleotide Sequencing
Sprache
eng
Medium
Electronic-eCollection
Online publication date
2014
Open access status
Open Access
Paginierung
e86869
Datum der Veröffentlichung
2014
Status
Published
Publisher licence
CC BY
Datum der Datenerfassung
2014
Titel
CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
Sub types
  • Comparative Study
  • research-article
  • Evaluation Study
  • Journal Article
Ausgabe der Zeitschrift
9

Files

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0086869&type=printable https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24466273/pdf/?tool=EBI https://europepmc.org/articles/PMC3899341?pdf=render

Data source: Europe PubMed Central

Abstract
The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorporates three different seed types, i.e. maximal exact match seeds, exact-match k-mer seeds and variable-length seeds, into the alignment pipeline. Furthermore, three techniques: weighted seed-pairing heuristic, paired-end alignment pair ranking and read mate rescuing have been conceived to facilitate accurate paired-end alignment. For base-space alignment, we have compared CUSHAW3 to Novoalign, CUSHAW2, BWA-MEM, Bowtie2 and GEM, by aligning both simulated and real reads to the human genome. The results show that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novoalign for short-reads with high error rates. For color-space alignment, CUSHAW3 is consistently one of the best aligners compared to SHRiMP2 and BFAST. The source code of CUSHAW3 and all simulated data are available at http://cushaw3.sourceforge.net.
Date of acceptance
2013
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/24466273
DOI
10.1371/journal.pone.0086869
eISSN
1932-6203
Externe Identifier
  • PubMed Central ID: PMC3899341
Ausgabe der Veröffentlichung
1
Zeitschrift
PLoS One
Schlüsselwörter
  • Base Sequence
  • Computational Biology
  • Computer Simulation
  • High-Throughput Nucleotide Sequencing
  • Sequence Alignment
  • Software
Sprache
eng
Country
United States
Paginierung
e86869
PII
PONE-D-13-23548
Datum der Veröffentlichung
2014
Status
Published online
Datum, an dem der Datensatz öffentlich gemacht wurde
2014
Titel
CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
Sub types
  • Comparative Study
  • Evaluation Study
  • Journal Article
Ausgabe der Zeitschrift
9

Data source: PubMed

Author's licence
CC-BY
Autoren
Hosting institution
Universitätsbibliothek Mainz
Sammlungen
  • DFG-OA-Publizieren (2012 - 2017)
Resource version
Published version
DOI
10.1371/journal.pone.0086869
Funding acknowledgements
  • DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin
File(s) embargoed
false
Open access
true
ISSN
1932-6203
Ausgabe der Veröffentlichung
1
Zeitschrift
PLoS one
Schlüsselwörter
  • 004 Informatik
  • 004 Data processing
Sprache
eng
Open access status
Open Access
Paginierung
e86869
Datum der Veröffentlichung
2014
Public URL
https://openscience.ub.uni-mainz.de/handle/20.500.12030/8026
Herausgeber
PLoS
Herausgeber URL
http://dx.doi.org/10.1371/journal.pone.0086869
Datum der Datenerfassung
2022
Datum, an dem der Datensatz öffentlich gemacht wurde
2022
Zugang
Public
Titel
CUSHAW3 : sensitive and accurate base-space and color-space short-read alignment with hybrid seeding
Ausgabe der Zeitschrift
9

Files

cushaw3___sensitive_and_accur-20220925163323120.pdf

Data source: OPENSCIENCE.UB

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