External databases

IMP3 makes use of external databases. They should be provided in or linked to one directory. See the install.

The following steps access external databases:

• Preprocessing:
  • adapter file for trimmomatic,
  • one or more genomes to filter against (optional),
  • sortmeRNA Silva database (metatranscriptomics only).
• Taxonomy:
  • a kraken2 database,
  • the GTDB-tk database (only, if binning is done),
  • the eukdetect (BUSCO) database (optional).
• Annotation:
  • HMM collections.