General Information
| Description | A fast versatile pipelined K-mer toolkit |
| Homepage | https://sourceforge.net/projects/kanalyze/ |
Publications
KAnalyze: a fast versatile pipelined K-mer toolkit
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.
Related Tools
Epigenomic k-mer dictionaries
Published May 2015
Shedding light on how sequence composition influences in vivo nucleosome positioning
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