VarCap: a new method for genotyping of prokaryotic populations
We created VarCap, a fully automated workflow that allows scientists to rapidly predict variants within high coverage, short read paired end sequencing data. VarCap automatically performs quality filtering, mapping, variant calling and post-filtering of the predicted variants. VarCap can be used for single organism as well as multi organism experiments as long as references are provided for the involved organisms . In order to allow a broad community to use VarCap, we implemented VarCap within our publicly available Galaxy server.
VarCap is designed to predict different allele frequencies in experimental evolution experiments, and it is able to detect and report the frequencies of multiple genotypes within clinical samples e.g., multiple infections.