Tomer Altman

@rcedgar I've posted screenshots of the VADR annotation to Slack a few times. We're getting comparable annotations to the standard NCBI annotations for the SARS-CoV-2 reference sequence. It won't be...

Especially for distantly-related CoVs.

This all might be academic because GenBank might show us the door. VADR is a tool used by NCBI for evaluating viral genome submissions, so I think we have a...

Kraken2 can do this, pretty sure! On June 21, 2020 8:46:07 AM PDT, Artem Babaian wrote: >I'm 100% on board with doing this analysis. We'll have a nice data-set >to...

Kraken reports the LCA of each kmer along the length of the read / contig. I can help make a custom DB of Coronavirus sequences See this: https://github.com/DerrickWood/kraken2/wiki/Manual A space-delimited...

I recommend the following: * Pull out all curated Nidovirales proteins from UniProt (aka the ones from SwissProt), which is n=~540 * Scrape out the Pfam annotations curated on those...

Tested, now documented too: https://github.com/ababaian/serratus/wiki/Creating-taxon-specific-slices-of-the-Pfam-HMM-database Currently integrating into DARTH, to make it easy for @rchikhi to run it on our divergent assemblies.

Implemented this in Darth on a separate branch, so that this doesn't interfere with the 'production' usage of Darth till this point. @rchikhi , please see new branch `nido-pfam`. I've...

Reassigning to @rchikhi to test as part of generating the genome structure plots.

Please search the genome against the full Pfam library using `--max -E 0.01` instead of `--cut_ga`. These are very distant proteins, and the HMMER3 heuristics will miss many of them.