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7 indexed repositories · View on GitHub

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

Jupyter Notebook · 559 stars
amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p...

C++ · 391 stars
egapx
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

Nextflow · 207 stars
icn3d
web-based protein structure viewer and analysis tool interactively or in batch mode

JavaScript · 175 stars
ncbi-cxx-toolkit-public
NCBI C++ Toolkit package sources

C++ · 102 stars
clinvar
ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at 'clinvar@ncbi.nlm.nih.gov...

HTML · 84 stars
stxtyper
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

C++ · 19 stars

Beginner friendly Everything

Open All

README correcting request. Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

ncbi/egapx#269 · Opened Sep 19, 2026
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
lds2_indexer not found during rnaseq_collapse Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

ncbi/egapx#267 · 1 comment · Opened Sep 4, 2026
Segmentation fault in rnaseq_collapse_new Open

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

ncbi/egapx#264 · 1 comment · Opened Aug 19, 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
How to increase parallelism of minimap2_wnode_fasta in EGAPx? Open

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

ncbi/egapx#263 · 3 comments · Opened Aug 8, 2026
Huge genome annotation issue Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

ncbi/egapx#262 · 16 comments · Opened Aug 4, 2026
COBALT: CMultiAligner::x_BuildAlignmentIterative double frees constraint hits when the alignment stage throws anything other than std::bad_alloc Open

Difficulty 1/5 Under an hour Newbie friendliness 88/100

ncbi/ncbi-cxx-toolkit-public#25 · 1 comment · Opened Aug 3, 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
Negative hmm scores throw an error in amr_report.cpp Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 68/100

ncbi/amr#192 · 2 comments · Opened Jun 29, 2026
amr_report crashes with "QC_ASSERT hmmStart" when multiple overlapping NCBIFAM HMM hits exist for a single protein (v4.2.7) Open

bug

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

ncbi/amr#191 · 1 comment · Opened Jun 19, 2026
Local SRA read cache isn't relocatable — read paths in sra_dir/runs.yaml are stored as absolute paths Open

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

ncbi/egapx#257 · 1 comment · Opened Jun 18, 2026
rnaseq_collapse fails with a CStringException::eConvert error Open

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

ncbi/egapx#256 · 9 comments · Opened Jun 15, 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
On the masking step Open

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

ncbi/egapx#253 · 3 comments · Opened Jun 5, 2026
Newer nextflow version (26.04.x) import errors Open

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

ncbi/egapx#251 · 1 comment · Opened Jun 2, 2026
Memory Configuration Issues for Large Genomes Open

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

ncbi/egapx#250 · 6 comments · Opened Jun 1, 2026
star_wnode writes ~5.5 TB of temporary files to disk when TMPDIR is set in slurm.config Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

ncbi/egapx#249 · 9 comments · Opened May 29, 2026
Segmentation fault in rnaseq_collapse Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

ncbi/egapx#246 · 9 comments · Opened May 14, 2026
‌Arabidopsis thaliana rnaseq_collapse Segmentation fault Open

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

ncbi/egapx#245 · 6 comments · Opened May 12, 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
please do reactive python binding via anywidget Open

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

ncbi/icn3d#129 · 3 comments · Opened Apr 16, 2026
Download genome as part of Offline mode? Open

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

ncbi/egapx#220 · 1 comment · Opened Apr 8, 2026
Isoform nomenclature question Open

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

ncbi/egapx#217 · 5 comments · Opened Mar 24, 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
windowmasker reads from a file called `-` instead of from `stdin`. Open

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

ncbi/ncbi-cxx-toolkit-public#21 · 7 comments · Opened Sep 19, 2025
Use of RNA-seq strand information in EGAPX pipeline Open

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

ncbi/egapx#172 · 12 comments · Opened Sep 8, 2025
BUG: Treats local read files as SRR, if it supplied as path to read list. Open

reads error

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

ncbi/egapx#165 · 19 comments · Opened Aug 25, 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
v1.0.31 binary shared object issue Open

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

ncbi/stxtyper#12 · 7 comments · Opened Jan 22, 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
Core dump when running multi-threaded on certain fa inputs Open

bug conda

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

ncbi/amr#145 · 4 comments · Opened Jul 9, 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
ClinVar API not returning the correct last_evaluated date for germline classification Open

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

ncbi/clinvar#8 · Opened Apr 11, 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

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