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This is a request to update the "genome coverage" [[OBI:0001939](http://purl.obolibrary.org/obo/OBI_0001939)]
**New parent term:** sequence data [[OBI:0000973](http://purl.obolibrary.org/obo/OBI_00…
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### Description of the bug
Viralrecon has worked perfectly for our SCV2 and some hybrid capture protocols (with the metagenomic side). However, when I ran the pipeline by passing a custom bed file an…
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I have 200 metagenomes extracted from stream biofilms. I binned contigs to obtain MAGs and I dereplicated MAGs obtained in all samples to obtain a final pool of MAGs. Finally I mapped reads from each …
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Motivated by https://github.com/nextstrain/pathogen-repo-guide/issues/50:
> It seems like a common pattern for sequencing efforts to focus on specific genes instead of the full genome. It would be…
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There seems to be a large KP.3.1.1+S:S31F branch, while KP.3.1.1 shall have S:31del.
That branch is driven by Denmark seqs which do not handle S:S31del well. When Querying C12616T, A13121T, C2165…
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Hi,
we recently sequenced a batch of 19 fungal isolates. I tried to assemble the genomes a few different ways (simplex + duplex or simplex corrected only) in order to figure out if there is still a…
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Currently, the coverage and alignment data are associated with the "Alignment profile" artifact, which contains a "none.biom" table. The features of the "none.biom" table are lineage strings, but the …
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is genome coverage related to both -b and -s ? I got 95% coverage with -b 1000 and -s {30,10},{100,100},{500,1000}.And l also tried {30,10},{100,100},{500,1000},{1000,5000} and {30,10},{100,100} . The…
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Dear Brent;
I build a customized genome sequence by adding a new sequence "VectorA" (~ 10kb) to hg19, and I would like to have coverage of the VectorA via your tool indexcov. I have tried different…
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Hi!
Thanks so much for developing tools like inStrain and dRep, they're very user-friendly. I have some questions regarding building the representative (rep) database. Initially, I used de novo ass…