Shoremap v3.0: Fast and accurate identifi cation of causal mutations from forward genetic screens

Abstract

Whole-genome resequencing of pools of recombinant mutant genomes allows direct linking of phenotypic traits to causal mutations. Such analysis, called mapping-by-sequencing, combines classical genetic mapping and next-generation sequencing by relying on selection-induced patterns within genome-wide allele frequency (AF) in pooled genomes. Mapping-by-sequencing can be performed with computational tools such as SHOREmap. Previous versions of SHOREmap, however, did not implement standardized analyses, but were specifi cally designed for particular experimental settings. Here, we introduce the usage of a novel and advanced implementation of SHOREmap (version 3.0), including several new features like fi le readers for commonly used fi le formats, SNP marker selection, and a stable calculation of mapping intervals. SHOREmap can be downloaded at shoremap.org.