SNP-sites¶
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
- HPC_SNP_SITES_BIN - executable directory