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Is there a way to select and download the plasmids of refseq?
Refseq has reference plasmid sequences that can be downloaded from `https://ftp.ncbi.nlm.nih.gov/genomes/refseq/plasmid/`.
They are …
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We should remove the reference genome field and replace it with an entry from the [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7408187/) resource.
The relevant information to store …
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Hi all,
Thanks for the development of this great tool !
I had a question related to getting both taxonomical information and genomes. Using the CLI, I managed to download all genomes for my taxon o…
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Apologies if this has been covered, if so please point me to the right place. I want to do a hybrid assembly with high coverage Illumina short insert reads and lower coverage ONT reads. My colleague s…
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Hi, I'm trying to build a UniVec_Core database. I keep running into this unable to match taxonomy targets error. I also tried to use taxID 28384 for all the univec_core sequences, just to see if that …
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Hello Fabio,
Thanks for developing the amazing riboWaltz package. I'm trying the codon_usage_psite using the following command, but get the error: "Error in h(simpleError(msg, call)) :
error in …
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:bug:
### :pencil: Describe the Issue
Ever since the introduction of the SRA Lite format, we've been plagued with TheiaProk failing in trimmomatic due to minimum quality errors. The SRA Lite…
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Previously we have been encouraging the use of the INSDC set of null terms when required:
| term | definition |
| ----- | ---------- |
| not applicable | information is inappropriate to report,…
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Hi,
We have been using ncbi datasets for 2 years and it works flawlessly, but this week it suddenly broke on seemingly Refseq IDs only.
e.g. `datasets download genome accession GCF_000806365.1…
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