ParDRe: faster parallel duplicated reads removal tool for sequencing studies

Publication type:
Journal article
Metadata:
Autoren
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000376656900019&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1093/bioinformatics/btw038
eISSN
1460-2059
Externe Identifier
  • Clarivate Analytics Document Solution ID: DM9AV
  • PubMed Identifier: 26803159
ISSN
1367-4803
Ausgabe der Veröffentlichung
10
Zeitschrift
BIOINFORMATICS
Paginierung
1562 - 1564
Datum der Veröffentlichung
2016
Status
Published
Titel
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
Sub types
  • Article
Ausgabe der Zeitschrift
32

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:title>Abstract</jats:title> <jats:p>Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe, a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files. It uses a novel bitwise approach to compare the suffixes of DNA strings and employs hybrid MPI/multithreading to reduce runtime on multicore systems. We show that ParDRe is up to 27.29 times faster than Fulcrum (a representative state-of-the-art tool) on a platform with two 8-core Sandy-Bridge processors.</jats:p> <jats:p>Availability and implementation: Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/pardre/</jats:p> <jats:p>Contact:  jgonzalezd@udc.es</jats:p>
Autoren
DOI
10.1093/bioinformatics/btw038
eISSN
1367-4811
ISSN
1367-4803
Ausgabe der Veröffentlichung
10
Zeitschrift
Bioinformatics
Sprache
en
Online publication date
2016
Paginierung
1562 - 1564
Datum der Veröffentlichung
2016
Status
Published
Herausgeber
Oxford University Press (OUP)
Herausgeber URL
http://dx.doi.org/10.1093/bioinformatics/btw038
Datum der Datenerfassung
2023
Titel
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
Ausgabe der Zeitschrift
32

Data source: Crossref

Abstract
<h4>Unlabelled</h4>Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe, a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files. It uses a novel bitwise approach to compare the suffixes of DNA strings and employs hybrid MPI/multithreading to reduce runtime on multicore systems. We show that ParDRe is up to 27.29 times faster than Fulcrum (a representative state-of-the-art tool) on a platform with two 8-core Sandy-Bridge processors.<h4>Availability and implementation</h4>Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/pardre/<h4>Contact</h4>jgonzalezd@udc.es.
Addresses
  • Grupo de Arquitectura de Computadores, Universidade da Coruña, Campus De Elviña, 15071, A Coruña, Spain and.
Autoren
DOI
10.1093/bioinformatics/btw038
eISSN
1367-4811
Externe Identifier
  • PubMed Identifier: 26803159
Open access
false
ISSN
1367-4803
Ausgabe der Veröffentlichung
10
Zeitschrift
Bioinformatics (Oxford, England)
Schlüsselwörter
  • Cluster Analysis
  • Sequence Analysis, DNA
  • Algorithms
  • High-Throughput Nucleotide Sequencing
Sprache
eng
Medium
Print-Electronic
Online publication date
2016
Paginierung
1562 - 1564
Datum der Veröffentlichung
2016
Status
Published
Datum der Datenerfassung
2016
Titel
ParDRe: faster parallel duplicated reads removal tool for sequencing studies.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
32

Data source: Europe PubMed Central

Abstract
UNLABELLED: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe, a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files. It uses a novel bitwise approach to compare the suffixes of DNA strings and employs hybrid MPI/multithreading to reduce runtime on multicore systems. We show that ParDRe is up to 27.29 times faster than Fulcrum (a representative state-of-the-art tool) on a platform with two 8-core Sandy-Bridge processors. AVAILABILITY AND IMPLEMENTATION: Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/pardre/ CONTACT: jgonzalezd@udc.es.
Date of acceptance
2016
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/26803159
DOI
10.1093/bioinformatics/btw038
eISSN
1367-4811
Ausgabe der Veröffentlichung
10
Zeitschrift
Bioinformatics
Schlüsselwörter
  • Algorithms
  • Cluster Analysis
  • High-Throughput Nucleotide Sequencing
  • Sequence Analysis, DNA
Sprache
eng
Country
England
Paginierung
1562 - 1564
PII
btw038
Datum der Veröffentlichung
2016
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2017
Titel
ParDRe: faster parallel duplicated reads removal tool for sequencing studies.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
32

Data source: PubMed

Autoren
Zeitschrift
Bioinform.
Artikelnummer
10
Paginierung
1562 - 1564
Datum der Veröffentlichung
2016
Titel
ParDRe: faster parallel duplicated reads removal tool for sequencing studies.
Ausgabe der Zeitschrift
32

Data source: DBLP

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