KAnalyze: a fast versatile pipelined K-mer toolkit

    loading  Checking for direct PDF access through Ovid

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:

Availability and implementation:

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

Contact:

fredrik.vannberg@biology.gatech.edu

Supplementary information:

Supplementary data are available at Bioinformatics online.

Related Topics

    loading  Loading Related Articles