Difference between revisions of "Ksnp"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_KSNP_BIN - executable directory | * HPC_KSNP_BIN - executable directory | ||
* HPC_KSNP_DOC - documentation directory | * HPC_KSNP_DOC - documentation directory | ||
Revision as of 21:21, 6 December 2019
Description
Description: identifies the pan-genome SNPs
Environment Modules
Run module spider Ksnp to find out what environment modules are available for this application.
System Variables
- HPC_KSNP_DIR - installation directory
- HPC_KSNP_BIN - executable directory
- HPC_KSNP_DOC - documentation directory
Citation
If you publish research that uses Ksnp you have to cite it as follows:
Gardner, S.N., T. Slezak, and B.G. Hall. 2015. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genomes. Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271.
Gardner, S.N. and Hall, B.G. 2013. When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760
Gardner, S.N. and Slezak, T.R. 2010. Scalable SNP analyses of 100+ bacterial or viral genomes. Journal of Forensic Research, 1:107.