README.md

egglet

A much reduced version of the eggNOG database for testing purposes.

To reduce size, the following procedure was followed:

1. Choose one of the smallest taxonomically restricted databases, thaNOG.
2. Arbitrarily select an orthologous group (OG) that is represented in thaNOG. The OG 1CB2I was chosen.
3. Using SQL, reduce the event, member, and og tables in the eggnog.db database to only a few entries each (see this script)
4. Find a fasta sequence represented in the OG (Nlim_1033 was chosen, with the sequence downloadable here). Shorten the sequence for querying.
5. Make a DIAMOND database from the single FASTA sequence using diamond makedb
6. Create a custom hmmpressed database from the HMM model for the OG 1CB2I at this link
7. In OG_fasta, remove most of the FASTA databases associated with OGs. Only keep 1CB2[A-Z].

Using this database depends on either using this functionality (also here) in eggnog-mapper to specify a data directory independently of the install directory, or copying tinyNOG/data into eggnog-mapper/data. For the first, add --data_dir ~/path_to/tinyNOG/data to the command line invocation of emapper.py.