Current status and where to go next:

[bethydavis]

Currently:

• Workflow to download the vertebrate, invertebrate, plant, mammalian, and rodent groups available on GitHub
• Limited entries to 2000 basepairs or less - no other restrictions
• Columns for: which group each entry comes from, and sequence length size, locus, taxonomy fields (superkingdom -> genus, organism = species)

Next:

• [ ] Decide where and how to host the downloaded database file (363 MB as .gz) - keep the groups separate and zipped for easier granularity for using specific groups
• [ ] Maine-eDNA wants the GitHub stuff on their repo
• [ ] Decide on an update schedule and point person (w compensation) to keep the database up to date (6-12 month re-download schedule?)
• [ ] Write a readme
• [ ] Write functions for users to search, filter, and download FASTA files for their own use @btupper
• [ ] Check with the group on ease of use (aka if the code is understandable) and any other functions or dbs needed @bethydavis
• [ ] Update the workflow flowcharts to the current process

[bethydavis]

Git LFS would have room for the db files on the Maine-eDNA repo, but still only adds a pointer reference to the file - won't actually host it directly

[btupper]

The README is a good place to document, but, as we get into the weeds, perhaps we should leverage the wiki? https://github.com/BigelowLab/referee/wiki