SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts


Summary: SpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein-level, optimizing its scores for matching very short sequences, and combining evidences from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes. Availability and implementation: SpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS at