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_Originally discussed in [Slack](https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1699928691378899)_
> In [reviewing dengue ingest](https://github.com/nextstrain/dengue/pull/13#discussion_r138734…
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Using ARIBA for gene detection, I tried to download the ncbi database with the following line
`ariba getref ncbi out.ncbi `
```
E-fetching 5795 genbank records from BioProject PRJNA313047 and w…
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I have been using nib-genome-download on anaconda3 environment for awhile. But since yesterday, I noticed that the download package is not working. It gives no error, just going black and nothing happ…
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Related to https://github.com/nextstrain/private/issues/102 and https://github.com/nextstrain/pathogen-repo-guide/issues/50
Writing out current methods for ingesting segmented viruses. These are sl…
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Hi Seeman,
I downloaded few plasmids sequences in Genbank full format from NCBI for plasmid annotation and ran the following command:
`prokka ENT2_Contig6_len_41186_circ_NDM-1_Plasmid.fasta --ou…
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I'm [creating a Tripal module](https://github.com/NAL-i5K/tripal_eutils) that imports NCBI XML and creates chado records, as well as linked records.
I think it would be neat to have a recommended, …
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Thankyou for building the new tool to complement Orthofinder.
The features are currently required in NCBI feature format. Is it possible to implement a feature to use a local GFF file instead as an i…
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When overwriting a zipped sbt with `sbt.save(sbt_file)`- either with a new one, or loading and adding to the existing sbt, I get an ignored exception.
Looks like is show up when different signatur…
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Can you please provide a script that takes two FASTA files as input and returns a single number: the intergenomic distance? We want to run this script on a global scale, comparing all ICTV exemplars n…
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Migrated from https://redmine.open-bio.org/issues/2819 which I filed on 2009-04-22,
> On their FTP site the NCBI provide a range of files for each genome/plasmid/chromosome, e.g.
ftp://ftp.ncbi.ni…