Accompanying dataset to the study "Natural CRISPR systems and targets in the human microbiome"

This repository hosts data products resulting from the CRISPR and cas gene study of the Human Microbiome Project (HMP1-II) population, consisting of spacer and repeat sequences (hmp1-II-crispr-spacers, hmp1-II-crispr-repeats) recovered from shotgun metagenomes using a read-based approach (Crass, Skennerton et al, 2013). The functional and taxonomic spacer annotations were obtained by aligning the spacer content to each sample’s metagenome and corresponding UniRef90 collection (hmp1-II-crispr-spacers-annotation).

We further provide the UniRef90 profiling of the 2,355 metagenomes of the HMP1-II collection that was used as the basis of the Cas1-Cas12 analysis (Files hmp1-II_uniref90 and hmp1-II_uniref90_cas). We used a custom HUMAnN 2 database to subset relevant protein families (humann2_cas_mapping).