New applications of next-generation sequencing (NGS) use pooled samples containing DNA from multiple individuals to perform population genetic analyses. SNPGenie is a Perl program which analyzes the variant results of a single-nucleotide polymorphism (SNP) caller to calculate evolutionary parameters, such as nucleotide diversity (including its nonsynonymous and synonymous partitions, πN and πS) and gene diversity. Variant calls are typically present in annotation tables and assume that the pooled DNA sample is representative of some population of interest. For example, if one is interested in determining the nucleotide diversity of a virus population within a single host, it might be appropriate to sequence the pooled nucleic acid content of the virus in a blood sample from that host. Comparing πN and πS for a gene product, or comparing gene diversity at polymorphic sites of different types, may help to identify genes or gene regions subject to positive (Darwinian) selection, negative (purifying) selection, and random genetic drift. SNPGenie also includes such features as minimum allele frequency trimming (see Options), and can be combined with upstream applications such as maximum-likelihood SNP calling techniques (e.g., see Lynch et al. 2014). For additional background, see Nelson & Hughes (2015) in the References.
module spider SNPGenie to find out what environment modules are available for this application.
- HPC_SNPGENIE_DIR - installation directory