Implement viral, fungal taxonomic profiling with sylph

[ppreshant]

Goal

Want to use sylph as a fast mode replacement for lemur in taxonomic_profiling

• For the paper, read more to see where sylph is a better fit: taxonomic_profiling or species detection?

Plan

• Once the sylph module and DBs are ready; Revive sylph module, download 3 DBs #73
• Add a switch for ~ order of interest ; options = prokaryotic (bacteria, archea) / virus / eukaryotic (fungi)
• connect it to chosing the DB for sylph in the nextflow.config or related config file..
• test with a small/subsampled microbiome dataset that contains all 3?

comments

Austin: Should be pretty straightforward!

• Just needs a database of viruses : Unified human gut virome catalog, IMG-B, .. ?
• Can also throw in lemur ; maybe do some comparison?