Tomer Altman
Tomer Altman
For the manuscript, we improved the assembly of all CoV/nido from novel taxa. But those improved assemblies have not made it over to `lovelywater`. Example using AmexNV: `aws s3 cp...
@asl @rcedgar To help coronaSPAdes identify CoV-associated contigs from the full assembly graph, we need to expand our set of target HMMs. Versions: 1. Pfam-SARS model HMMs 2. (current) All...
Here's what NCBI has to say about assigning a meaningful entry for the "source" of the sequence material in the face of uncertainty: https://www.ncbi.nlm.nih.gov/books/NBK53701/#gbankquickstart.can_i_use_the_word__unkn So we need to come up...
From the Handbook: https://www.ncbi.nlm.nih.gov/books/NBK53714/#gbankquickstart.i_have_viral_sequence_da - [ ] CDS feature(s) with product name(s), nucleotide locations, and amino acid translation(s) of all coding regions (showing start and stop codons, if present) -...
As per: https://www.ncbi.nlm.nih.gov/books/NBK53709/#gbankquickstart.when_is_tbl2asn_a_good_a In the following section: > B. Create a Submission Template file: They describe using an online tool to auto-generate an ASN.1 text file with the project meta-data...
As per: https://www.ncbi.nlm.nih.gov/books/NBK53709/#gbankquickstart.when_submitting_to_genba My feeling is that it would make our submission better organized if each submission was tied back to a common NCBI BioProject ID.
From the Handbook: https://www.ncbi.nlm.nih.gov/books/NBK53714/#gbankquickstart.i_have_viral_sequence_da A related entry from the Handbook: https://www.ncbi.nlm.nih.gov/books/NBK53701/#gbankquickstart.Viral_Source_Material - [ ] A unique name - [ ] Country where virus was collected (if known) - [ ]...
In order to automate a bulk submission to NCBI, we need to use `tbl2asn`: https://www.ncbi.nlm.nih.gov/books/NBK53709/#gbankquickstart.when_is_tbl2asn_a_good_a https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ We'll add a step to the Darth annotation pipeline to auto-create the ASN.1 file,...
Hi Derrick, I've been using Kraken as of late, and decided to incorporate some fixes. First, I incorporated a suggested fix by Silas Kieser for downloading the human genome, and...
Fixed a few statements in the Makefile, and updated the .gitignore file for the new executable.