search

lentendu / DeltaMP

A flexible, reproducible and resource efficient metabarcoding amplicon pipeline for HPC
GNU General Public License v3.0
2 stars 1 forks source link

Feature: provide manually curated reference sequences to use for taxonomic identification #176

Closed lentendu closed 5 months ago

lentendu commented 1 year ago

Need to check the different scenari:

  1. long new and long ref --> IDDEF=2, no end-gaps, no problem
  2. long new and short ref --> IDDEF=1, need to cut new, at which step?
  3. short new and short ref --> IDDEF=1, might be an issue if new are incomplete Sanger seq with missing region near the primers
  4. short new and long ref --> IDDEF=2, not an issue as new will work well even without end-gap

Then assemble database in the output directory and update DB and DBFOLD, and DBCUT if needed --> to do at the beginning of id step

If DBADD, just check in deltamp that taxonomy ranks matches.