SHOREmap v3.0: fast and accurate identification of causal mutations from forward genetic screens

Methods in Molecular Biology
Hequan Sun, Korbinian Schneeberger

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.

Citations

Apr 24, 2016·Nucleic Acids Research·Sergio Pulido-TamayoKathleen Marchal
Nov 18, 2018·The Plant Journal : for Cell and Molecular Biology·Florian DöringPeter Westhoff
Apr 26, 2017·Frontiers in Plant Science·Biyun ZhuDaoxin Xie
Mar 30, 2020·Current Biology : CB·María José de LeoneMarcelo J Yanovsky
Apr 2, 2021·The Plant Cell·Nicholas J ProvartAnn E Loraine
Nov 2, 2021·Frontiers in Plant Science·Mona MaparMartin Hülskamp

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