Dr. White's lab emails:
Jose Figueroa <jlfiguer@charlotte.edu>,
Joshua Hensley <jhensl19@charlotte.edu>,
Madeline Bellanger <mbellang@charlotte.edu>,
Andra Buchan <abuchan@charlotte.edu>,
Andrew Redinbo <aredinbo@charlotte.edu>,
Stephanie Wiedman <swiedma1@charlotte.edu>

Nowlan and I met with Joshua (Josh) Hensley <jhensl19@charlotte.edu> on Wednesday (Sep 18) to discuss which files should be used to create this documentation.

For context, we've found Metacerberus output (genomes (.fna) and annotations (.gff)) on their GitHub page that we're able to view in IGB, but it's variable whether that output is behaving properly depending on which .fna and .gff files I grab. Is this an issue with Metacerberus having variable output that we'll need to account for, or was I simply unable to find an example of typical Metacerberus output?

Next steps: Get sample output from Josh that we can use for the documentation. He is also looking into the possible variability of this output for us.

We've discovered the issue we were experiencing with the Metacerberus output and wrote up our findings in IGBF-3924. Josh has provided us with sample output which we can use to create the documentation, here's the link to it on Google Drive: https://drive.google.com/drive/folders/14noPsmKYMxX9jgHYQhkjqaTGzT8z8bSK

Basic outline:

1. How to add a custom genome (using the lambda phage genome on Metacerberus' GitHub as an example: https://github.com/raw-lab/MetaCerberus/blob/main/lib/dependency_files/lambda-phage.fna)
2. How to open files in IGB (local and remote)
3. Caveat about Lambda_phage_sequences.gff files and how to fix the issue.

I've created a MetaCerberus page within the IGB User's Guide (https://wiki.bioviz.org/confluence/display/igbman/MetaCerberus). I've also created IGB documentation for MetaCerberus' GitHub (https://drive.google.com/file/d/1lPyZ-dI4gSYOHrrygVY9R88KH7sCH2zk/view?usp=sharing).

However, as a result of this ticket, we now know that both the GFF and GTF parsers need updating before MetaCerberus users can reliably visualize their output in IGB.

Next steps:

• Send IGB documentation to Josh to publish on GitHub.
• Send Rick a summary of what we've learned and offer to meet with him to walk him through visualizing data in IGB.
• Upgrade the GFF and GTF parsers, then update both sets of documentation to remove the caveat about ##FASTA sections.

Nowlan Freese, any other next steps you can think of? If not, I will start working on these tasks and move this ticket to the backlog until we complete those blocker tickets.

After chatting with Dr. Freese, I am going to make the following changes to our documentation and then close this ticket:

• Be more verbose in my description of adding custom genomes to IGB (e.g., "The fasta file used with metacerberus will need to be added as the genome to IGB).
• Add a second major heading for visualizing output in IGB, then make the others subheadings.
• Add picture to final section of what the output will look like in IGB.
• Add table of contents.