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loculus-project / loculus

An open-source software package to power microbial genomic databases
https://loculus.org
GNU Affero General Public License v3.0
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How to handle seqs that INSDC doesn't accept (gappy)? #2794

Open chaoran-chen opened 1 month ago

chaoran-chen commented 1 month ago

As discussed in our last meeting, we would like to investigate how to handle seqs that INSDC doesn't accept (gappy).

emmahodcroft commented 5 days ago

To clarify: These are incomplete sequences (fragments along a genome) that are not accepted by INSDC (wants you to submit every fragment separately), but would be accepted by Pathoplexus.

However this is something we've heard from others and as of today haven't tested ourselves - we should test & then reach out to get more info from INSDC/ENA etc about this issue.

And then we need to have a convo about how we may or may not want to resolve or give info about this (if we can't pass these on) on our website docs somehow.