Ask VEuPathDb for reference sync with NCBI

[nekrut]

Contact VEuPathDb about syncing references with NCBI

[d-callan]

Some things to think about prior to a call:

1. maybe putting together a list, in a google sheet or other format share-able w them, of what all assemblies of theirs dont match the GCA accession they claim (and which of these are in our list of initial targets)
2. it might be possible to do some interesting things in spite of these out-of-sync issues.. ex: a first step might be to let ppl run galaxy workflows on the assembly claimed by the gca accession regardless of whether its identical to whats actually in ncbi and then pass back to veupath gene identifiers rather than loci. their jbrowse tracks wouldnt work, but some other plots would id think.
3. they might have thoughts on our initial organisms list too. ive done my best to include what i remember as big ones, in addition to what anton had already, but they might have a couple theyd really like to be able to let ppl run galaxy workflows on. are we open to that feedback?
4. how much does it really matter what theyre claiming as reference? as long as we also have that assembly in addition to the ncbi refseq? is this a 'let the user decide' type moment? maybe ive misunderstood something..

[nekrut]

Here is a link to slides from the meeting: https://docs.google.com/presentation/d/1JDHoirXmqb6ovHW-eKWq232alnI_Ro2yb_6c5PQdM5U/edit?usp=sharing

The next steps are:

• Vamsi to provide list of genomes where ViewPathDB and GenBank sequences differ.
• Terrence/NCBI team to allocate staff time (estimated 1 week) to analyze and categorize genome discrepancies.
• ViewPathDB team to provide usage statistics to help prioritize genomes for analysis.
• Anton to follow up in second week of January to schedule next meeting on genome reconciliation.
• ViewPathDB team to discuss internally about adding links to BRC Analytics tools.
• BRC Analytics team to implement sequence identifier mapping between ViewPathDB and GenBank accessions.