CasCollect: Detecting cas genes and CRISPR arrays in raw sequence data v1

Abstract

This software examines raw Illumina sequence data files for cas genes and CRISPR arrays, either to be used as evidence of genome editing or for basic analysis of bacterial genomes. It translates sequencing reads into peptide sequences, and runs these against sensitive hidden Markov models for numerous Cas protein families. The set of hit read seeds is then expanded leftward and rightward by sequence matching to remaining reads, and after multiple cycles, this small fraction of the original reads is assembled to produce Cas operons. A separate mode using known CRISPR repeat sequences for a genus are used to identify CRISPR arrays that may be in genomic locations that are isolated from Cas genes.SAND2019-11770 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.