SHRiMP

Gene Sequence Alignment Software

High-throughput Next Generation gene sequencing platforms currently produce several hundred million reads per sequencing run. SHRiMP is one of many tools that can be used for the alignment of short read sequences against known reference genomes. SHRiMP utilizes gapped q-gram filtering and Smith-Waterman methods for accurate sequence alignments. And it generates statistical data for assessing probability metrics of homologous gene sequence alignments.

SHRiMP software is available to CSU researchers on the Bioinformatics database server.