ncbi/datasets

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NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Stars: 559
Forks: 70
Open beginner issues: 0
Indexed issues: 25
Avg merge: 1m
Merged PRs (30d): 2

Dominant language: Jupyter Notebook
License: No license data
Last GitHub push: Sep 9, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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25 open issues indexed

Feature request: provide assembly summary metadata in Parquet format on the fast-download servers, downloadable via datasets CLI Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

ncbi/datasets#605 · 1 comment · Opened Sep 15, 2026
Fetch genes by assembly ID OR fetch genome annotation report using the CLI Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

ncbi/datasets#600 · 2 comments · Opened Aug 16, 2026
Inconsistent host annotation for ON022733.1 in datasets CLI and NCBI website Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

ncbi/datasets#595 · 5 comments · 1 reaction · Opened Jul 28, 2026
datasets summary virus genome taxon 10239 fails on gateway errors Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

ncbi/datasets#594 · 4 comments · Opened Jul 23, 2026
Add metadata column to distinguish patent sequences (e.g. include Genbank division) Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ncbi/datasets#586 · 1 comment · Opened Jun 11, 2026
filter by segmant Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 48/100

ncbi/datasets#578 · 3 comments · Opened May 11, 2026
`Error: net/http: TLS handshake timeout` Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

ncbi/datasets#568 · 1 comment · Opened Mar 17, 2026
Enhancement request: Support multi-host and host-exclusion filtering in NCBI Datasets CLI (viral genomes) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

ncbi/datasets#559 · 1 comment · Opened Jan 29, 2026
Date ranges (e.g., 2014/2019) are incorrectly parsed as single year in metadata Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

ncbi/datasets#557 · 2 comments · Opened Jan 26, 2026
support for gene_type Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ncbi/datasets#544 · 2 comments · Opened Dec 1, 2025
`Error: Download error: stream error: stream ID 5; INTERNAL_ERROR; received from peer` is back Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

ncbi/datasets#541 · 1 comment · Opened Nov 24, 2025
ncbiSraAccessions occasionally contain sample accessions (ERS) instead of the usual run accessions (SRR/ERR/DRR) Open

bug

Difficulty 5/5 Over a week Newbie friendliness 25/100

ncbi/datasets#516 · 2 comments · Opened Jul 21, 2025
Author lists do not deduplicate authors with differing numbers of initials Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

ncbi/datasets#508 · 1 comment · Opened Jun 24, 2025
Build fails on ARM windows 11 with "No matching toolchains found for types: @@aspect_bazel_lib+//lib:copy_to_directory_toolchain_type" Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ncbi/datasets#496 · 3 comments · Opened May 27, 2025
Please add --released-before to `datasets download virus genome taxon` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

ncbi/datasets#489 · 1 comment · 1 reaction · Opened May 20, 2025
`datasets summary genome taxon` should have exitcode of `0` when there are no genomes for a valid taxon Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

ncbi/datasets#482 · 5 comments · 2 reactions · Opened May 8, 2025
found incorrect/missing assembly_link_type Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

ncbi/datasets#436 · 1 comment · Opened Dec 10, 2024
Support for non-Refseq genes Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

ncbi/datasets#434 · 1 comment · 1 reaction · Opened Dec 6, 2024
Include corresponding gca/gcf accession in the metadata of each sample Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ncbi/datasets#433 · 5 comments · 1 reaction · Opened Dec 5, 2024
"Total" sequence length doesn't include organelles Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 40/100

ncbi/datasets#403 · 1 comment · Opened Sep 17, 2024
"/note" feature retrieving through command lines Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ncbi/datasets#389 · 4 comments · Opened Jul 31, 2024
How to download genome annotation report Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 28/100

ncbi/datasets#379 · 1 comment · Opened Jun 20, 2024
Download error for list of WP accessions Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ncbi/datasets#372 · 12 comments · Opened Jun 3, 2024
Add publication info to assembly or BioProject fields. Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

ncbi/datasets#369 · 2 comments · Opened May 24, 2024
`Submitter Names` lack spaces in `dataformat tsv virus-genome` compared to genbank file serialization Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ncbi/datasets#336 · 1 comment · Opened Mar 21, 2024

ncbi/datasets

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