Phage toolkit to detect and assemble phage candidates for phage therapy. Snakemake workflow using Snaketool to assemble and annotate phage sequences.

This snakemake workflow was built using Snaketool, to assemble and annotate phage sequences. Currently this tool is being developed for phage genomes. THe steps include

  • QC using Trimanammi
  • Assembly, either SPAdes or Flye
  • Contig quality checks
    • Read coverage using Koverage
    • Verify they are viral contigs using ViralVerify
    • Completeness using CheckV
    • Assembly graph compnents check - internal script This results in determining if the phage genome was assembled
  • Annotation of the phage genome using Pharokka