MersV1, Main, Exploration, bibRecord, 001C08

KAnalyze: a fast versatile pipelined K-mer toolkit

Identifieur interne : 001C08 ( Main/Exploration ); précédent : 001C07; suivant : 001C09

KAnalyze: a fast versatile pipelined K-mer toolkit

Auteurs : Peter Audano ; Fredrik Vannberg

Source :

Bioinformatics [ 1367-4803 ] ; 2014.

RBID : PMC:4080738

Descripteurs français

KwdFr :
- Algorithmes, Analyse de séquence d'ADN (), Chromosomes humains de la paire 1 (), Humains, Logiciel.
MESH :
- Algorithmes, Analyse de séquence d'ADN, Chromosomes humains de la paire 1, Humains, Logiciel.

English descriptors

KwdEn :
- Algorithms, Chromosomes, Human, Pair 1 (chemistry), Humans, Sequence Analysis, DNA (methods), Software.
MESH :
- chemistry : Chromosomes, Human, Pair 1.
- methods : Sequence Analysis, DNA.
- Algorithms, Humans, Software.

Abstract

Motivation: Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language.

Results: As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes.

Availability and implementation: KAnalyze is available on SourceForge:

https://sourceforge.net/projects/kanalyze/

Contact:fredrik.vannberg@biology.gatech.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080738

DOI: 10.1093/bioinformatics/btu152
PubMed: 24642064
PubMed Central: 4080738

Affiliations:

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<front><div type="abstract" xml:lang="en"><p><bold>Motivation</bold>
: Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language.</p>
<p><bold>Results</bold>
: As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes.</p>
<p><bold>Availability and implementation</bold>
: KAnalyze is available on SourceForge:</p>
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<p><bold>Contact:</bold>
<email>fredrik.vannberg@biology.gatech.edu</email>
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<p><bold>Supplementary information</bold>
: <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/lookup/suppl/doi:10.1093/bioinformatics/btu152/-/DC1">Supplementary data</ext-link>
 are available at <italic>Bioinformatics</italic>
 online.</p>
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KAnalyze: a fast versatile pipelined K-mer toolkit

KAnalyze: a fast versatile pipelined K-mer toolkit

Source :

Descripteurs français

English descriptors

Abstract

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Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

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Pour générer des pages wiki

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