KAnalyze
KAnalyze is a Java-based software tool designed to convert nucleotide sequences into k-mers, short overlapping fragments of uniform length, commonly used in bioinformatics applications. KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read, and process large datasets with 2 GB of memory. The tool outperforms existing k-mer counters such as Jellyfish, DSK, and a Perl/Linux utilities pipeline. KAnalyze is available on SourceForge and its command-line interface (CLI) is designed to integrate into pipelines written in any language.
Topic
Nucleic acids;RNA;DNA;Sequence analysis
Detail
Operation: Nucleic acid sequence analysis
Software interface: Command-line user interface
Language: Java
License: GNU GENERAL PUBLIC LICENSE v3
Cost: Free
Version name: 0.9.7
Credit: Georgia Institute of Technology.
Input: -
Output: -
Contact: fredrik.vannberg@biology.gatech.edu
Collection: -
Maturity: -
Publications
- KAnalyze: a fast versatile pipelined k-mer toolkit.
- Audano P and Vannberg F. KAnalyze: a fast versatile pipelined k-mer toolkit. KAnalyze: a fast versatile pipelined k-mer toolkit. 2014; 30:2070-2. doi: 10.1093/bioinformatics/btu152
- https://doi.org/10.1093/bioinformatics/btu152
- PMID: 24642064
- PMC: PMC4080738
Download and documentation
Documentation: https://github.com/shashidhar22/kXpRESs/blob/master/kanalyze-0.9.7/KAnalyzeManual.pdf
Home page: http://vannberg.biology.gatech.edu:8080/VannbergLab/kanalyze.html
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