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.