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Kmer-SSR

Kmer-SSR is a tool to detect simple sequence repeats (SSRs) in genomic sequences. The Kmer-SSR algorithm has an option for an exhaustive search.

Topic

Sequence composition, complexity and repeats; Sequence analysis; Sequencing

Details

Operation: Repeat sequence detection
Input: FASTA
Output: Tab-delimited (.tsv)
Software interface: Command-line user interface
Language: C++
Operating system: Linux
License: Not stated

Cost

Version name: -

Credit: Brigham Young University and the Department of Biology
Contact: perry.ridge _at_ byu.edu
Collection: -

Publications

Pickett BD, Miller JB, Ridge PG "Kmer-SSR: a fast and exhaustive SSR search algorithm." Bioinformatics. 2017 Dec 15;33(24):3922-3928. https://doi.org/10.1093/bioinformatics/btx538
PMID: 28968741
PMCID: PMC5860095

Download and documentation

Source: https://github.com/ridgelab/Kmer-SSR
Documentation: https://github.com/ridgelab/Kmer-SSR/blo
b/master/README
Home page: https://github.com/ridgelab/Kmer-SSR

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