Rhodopsin search in assemblies

This repository contains a Snakemake pipeline for detecting and annotating rhodopsin-like ORFs from genome assemblies.

Required inputs

1. Assemblies in FASTA format: input/{assembly}.fasta
2. Databases:
   • BLAST database sequence file: databases/{database}.faa
   • Marker file used for workflow discovery: databases/{database}.faa.pdb

Main outputs

• Final tables: output/{assembly}.tsv
• Intermediate results:
  • analysis/getorf/{assembly}.fasta
  • analysis/opsinmaphmm/{assembly}/
  • analysis/blast/{assembly}/{database}.txt

Deploy

snakedeploy deploy-workflow https://github.com/BejaLab/opsinsearch-assemblies project_name --branch main

Run

Using the provided profile:

snakemake --cores 8

Config parameters (config/config.yaml)

• pos: reference residue positions used by mapping logic
• hmm_score: minimum HMM score threshold
• blast_evalue: maximum BLAST e-value threshold
• mapping_score: minimum residue mapping score threshold