SpacerExtractor v0.9

Abstract

The SpacerExtractor tool is meant to robustly identify and extract CRISPR spacers from metagenome short reads. Working from a database of known CRISPR repeats, SpacerExtractor quickly scans short reads for the corresponding repeat sequences, extract the potential spacer between two repeats, apply several quality control, denoising, and clustering steps, and provides a full non-redundant complement of spacers for each detected repeat. Because of the high variability observed at CRISPR loci, this read mining approach typically recovers a much larger diversity of spacers than can be found in assembled contigs. SpacerExtractor also includes commands to run CRISPR-Cas Typer on a new set of genomes or MAGs, and add newly predicted repeats to the repeat database.