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ncbi
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
Downloading dehydrated genome datasets fails with a request timeout. command: `datasets download genome taxon Viridiplantae --annotated --assembly-level chromosome,complete_genome,scaffold --dehydrated --exclude-rna --exclude-seq --reference --filename viridiplantae.zip` expected: viridiplantae.zip with ncbi_dataset directories for...
Hi, very interesting project. I have installed in a conda env (with python 3.6.12) with: `pip install ncbi-datasets-pylib` I think that now I need to configure it with the script...
Hello, I'm trying to download the SAR2/human/USA dataset on an Linux/ARM64, for which there is no pre-compiled 'datasets' command line command. I've run into an issue, using R: ``` library(ncbi.datasets)...
Brad, I don't know if this is appropriate (?) or even possible to request here. So let me know if not. I didn't see any instructions for contributions in the...
Hi all, Thank you for your continued development of a terrific set of tools! We have been using v13 (v13.43.2) of NCBI Datasets via the CLI to access gene summary...
datasets version: 3.42.1 command: `datasets download genome accession GCA_000302695.1 --include-gbff` Results: ``` ├── ncbi_dataset │ └── data │ ├── assembly_data_report.jsonl │ ├── dataset_catalog.json │ └── GCA_000302695.1 │ ├── GCA_000302695.1_LSJC7_1.0_genomic.fna │ ...
I am trying to download genome of assembly level '**chromosome**' for several bacterial taxon. But realized that there were less number of total genomes being downloaded. I cross-checked the number...
**Describe the bug** The `Submitter Names` field has a not-very-robust serialization format of `LAST NAME,FIRST NAME INITIALS,LAST NAME,FIRST NAME INITIALS...` that does not separate individuals. Is this on purpose, if...
Unfortunately some of the valuable metadata contained in genbank files is lost on the way to datasets. In particular crucial author/submitter metadata is lost. Things like: `TITLE`, `JOURNAL`, `PUBMED` and...
Quite frequently, valuable metadata is contained in the genbank file field '/note`. Unfortunately, this field seems to get lost on the way to 'datasets download virus genome' Consider the metadata...