NgsTools: methods for population genetics analyses from next-generation sequencing data.

ABSTRACT:

Summary

Next-generation sequencing technologies produce short reads that are either de novo assembled or mapped to a reference genome. Genotypes and/or single-nucleotide polymorphisms are then determined from the read composition at each site, which become the basis for many downstream analyses. However, for low sequencing depths, e.g. , there is considerable statistical uncertainty in the assignment of genotypes because of random sampling of homologous base pairs in heterozygotes and sequencing or alignment errors. Recently, several probabilistic methods have been proposed to account for this uncertainty and make accurate inferences from low quality and/or coverage sequencing data. We present ngsTools, a collection of programs to perform population genetics analyses from next-gene

SUBMITTER: Fumagalli M 

PROVIDER: S-EPMC4016704 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature