Genome comparisons of crAss-like phages

About

This repo provides HMMs for hallmarks genes (MCP, Portal, and TerL) as well as a basic bash script (crAss.sh) that we used in our recent study to search for crAss-like phages. These can easily be used to search through metagenomes/contigs for the presence of putative crAssphages using just as single command (see below). The provided script will be updated on a regular basis, and will soon be provided in the form of a nextflow pipeline.

Usage

For the script to run successfully users need to install both Prodigal and HMMER beforehand.

To test if all dependencies are installed and executable, users may run the crAss.sh script using these HMM profiles, as well as this contig file with .fasta extension. Please make sure that all these files are in the same directory. Note that the HMM profiles require to get converted to binary compressed datafiles using hmmpress, using the following command:

hmmpress *.HMM

This will create a set of files with extensions: .h3m .h3i .h3f and .h3p

Once done users may execute the crAssZA.sh script as follows:

(crAss)[user@machine007]$ ./crAss.sh

Once executed, the script will run for a few seconds and set of output files will be generated. These will have extentions faa and hmmout that may require further manual inspection.