ZongzhiWu/phage_contig_annotator

Annotates genes on putative phage contigs with protein orthologous groups using PHROGs

█▀▀█ █░░█ █▀▀█ █▀▀▀ █▀▀   █▀▀ █▀▀█ █▀▀▄ ▀▀█▀▀ ░▀░ █▀▀▀   █▀▀█ █▀▀▄ █▀▀▄ █▀▀█ ▀▀█▀▀ █▀▀█ ▀▀█▀▀ █▀▀█ █▀▀█ 
█░░█ █▀▀█ █▄▄█ █░▀█ █▀▀   █░░ █░░█ █░░█ ░░█░░ ▀█▀ █░▀█   █▄▄█ █░░█ █░░█ █░░█ ░░█░░ █▄▄█ ░░█░░ █░░█ █▄▄▀ 
█▀▀▀ ▀░░▀ ▀░░▀ ▀▀▀▀ ▀▀▀   ▀▀▀ ▀▀▀▀ ▀░░▀ ░░▀░░ ▀▀▀ ▀▀▀▀   ▀░░▀ ▀░░▀ ▀░░▀ ▀▀▀▀ ░░▀░░ ▀░░▀ ░░▀░░ ▀▀▀▀ ▀░▀▀

Annotates genes on putative phage contigs with a database of hidden markov models (HMMs) based on PHROGs. This tool was built to support visual confirmation of predictions made by Jeager.

installation

1. clone the repository git clone https://github.com/Yasas1994/phage_contig_annotator.git && cd phage_contig_annotator
2. create a conda environment conda env create -f environment.yml
3. install phage_contig_annotator pip install .
4. download database phage_contig_annotator download_db

usage

conda activate phage_contig_annotator 
phage_contig_annotator --cpus 10 runall --contigs --input input_fasta_file_with_contigs --output output_dir

examples