-
Notifications
You must be signed in to change notification settings - Fork 34
Serratus Annotation
All darth annotations are in :
s3://serratus-public/seq/cov5/annotations.nt_otus.id99/
For PFAM alignments, make sure to only download *.darth.alignments.fasta and disregard the *.pfam.alignments.fasta and *.transeq.alignments.fasta. The .darth.alignments.fasta files correspond to the transeq/alignments.fasta file (which handles multi-contig assemblies) inside the Darth folder, when it exists, and otherwise pfam/alignments.fasta (which was made for single-contig assemblies).
Date of full run: 26-07-2020
All darth/serratax/serraplace annotations for the master table assemblies are in
s3://serratus-public/assemblies/annotations/
Same remark as above. For alignments, take *.darth.alignments.fasta.
Date of full run: 27-07-2020
Note: some annotations are also present in s3://serratus-public/assemblies/other/[accession].coronaspades/. Please disregard those, as they're only for Checkv-filtered assemblies, not the for BGC-filtered assemblies present in the master table.
(with emphasis on methods able to handle frameshifts/indels/ribosome slippage)
- FragGeneScan: https://academic.oup.com/nar/article/38/20/e191/1317565
-
GATU (U of Victoria!) https://4virology.net/virology-ca-tools/gatu/
NCBI Submission instructions for viruses: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/docs/submit/#submit_other_viruses
Here are some specific viral annotation resources to consider:
https://www.viprbrc.org/brc/home.spg?decorator=vipr [a nexus for virus pathogen resources]
*** https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov [specific information in ViPR on SARS-CoV-2, contains more than 1,607 genomes with Genbank Accession numbers] ***
https://www.viprbrc.org/brc/vigorAnnotator.spg?method=ShowCleanInputPage&decorator=corona [VIGOR4 viral genome ORF predition developed by JCVI]
https://www.ncbi.nlm.nih.gov/genome/viruses/ [a useful resource for viral genomics including links to database]
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381048/ [this paper is very relevant to viral ORF prediction]
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2606-y [lightweight viral annotation pipeline]
https://msphere.asm.org/content/3/2/e00069-18 [a viral annotation database cured from NCBI with manual refinement]