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The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP -the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methodsdoi:10.1371/journal.pcbi.1000386 pmid:19461883 pmcid:PMC2678294 fatcat:xi2byt525vdxbbyr7dwk3phrpu