DSK¶
Description¶
DSK is a k-mer counting software, similar to Jellyfish. DSK can be executed on any machine (only 1 GB memory required for a mammalian dataset) with reasonably low temporary disk usage, and supports any value of k. DSK can count k-mers of large Illumina datasets on laptops and desktop computers.
Environment Modules¶
Run module spider dsk
to find out what environment modules are available for this application.
Environment Variables¶
- HPC_DSK_DIR - installation directory
- HPC_DSK_BIN - executable directory
- HPC_DSK_DOC - documentation directory
- HPC_DSK_EXE - examples directory
Citation¶
If you publish research that uses dsk you have to cite it as follows:
Rizk, G., Lavenier, D., & Chikhi, R. (2013). DSK: k-mer counting with very low memory usage. Bioinformatics, 29(5), 652–653. https://doi.org/10.1093/bioinformatics/btt020
Categories¶
biology, ngs