KAnalyze: a fast versatile pipelined k-mer toolkit.
Bioinformatics
; 30(14): 2070-2, 2014 Jul 15.
Article
em En
| MEDLINE
| ID: mdl-24642064
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/.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Análise de Sequência de DNA
Limite:
Humans
Idioma:
En
Ano de publicação:
2014
Tipo de documento:
Article