SHOREmap v3.0: Fast and Accurate Identification of Causal Mutations from Forward Genetic Screens

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1284)

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 specifically 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 file readers for commonly used file formats, SNP marker selection, and a stable calculation of mapping intervals. SHOREmap can be downloaded at shoremap.org.

Key words

Forward genetics Bulk segregant analysis Next-generation sequencing Mapping-by-sequencing SNP marker Allele frequency analysis 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Plant Developmental BiologyMax Planck Institute for Plant Breeding ResearchCologneGermany

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