Viral heliorhodopsins pipeline

This repository contains the Snakemake workflow used for the bioinformatic analyses for the paper Hososhima et al (2022) "Proton-transporting heliorhodopsins from marine giant viruses" eLife.

All of the dependencies are taken care of with conda, so it is recommended to run snakemake with --use-conda.

This repository is organized as follows:

• analysis -- contains the intermediate files
• annotations -- manually curated data
• databases -- includes Pfam databases and algal protein sequences. To run the workflow from scratch, the soft link databases/Pfam should point to the Pfam database folder and soft links in databases/algae should point the corresponding fasta files.
• output -- final output files
• proteins -- curated sequence data for algal and viral heliorhodopsins
• viruses -- GenBank files with the viral genomes
• workflow -- workflow files, including:
  • envs -- conda environment files
  • Snakefile -- the snakemake file
  • scripts -- folder with scripts

The output files are as follows:

• cat_phylogeny.pdf -- concatenation phylogeny of the viruses
• EhVHeRs.tsv -- distribution of heliorhodopsin genes among EhVs
• HeR_tree.jtree -- phylogenetic tree of viral and algal heliorhodopsins in .jtree format
• HeR_tree.pdf -- image version of the same tree
• miniset_chronos.pdf -- small HeR tree with alignment of critical positions
• orthogroups.tsv -- EhV orthogroups