Difference between revisions of "SNP-sites"
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Variant Calling]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|snp-sites}} | |{{#vardefine:app|snp-sites}} | ||
Latest revision as of 12:56, 15 August 2022
Description
We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
Environment Modules
Run module spider snp-sites to find out what environment modules are available for this application.
System Variables
- HPC_SNP-SITES_DIR - installation directory
Citation
If you publish research that uses snp-sites you have to cite it as follows: