# kblin/ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

Repository: https://github.com/kblin/ncbi-genome-download
Canonical: https://ross.abutalabs.com/products/ncbi-genome-download
Language: Python
License: Apache-2.0
License Family: permissive
Topics: ncbi, bioinformatics, download-genomes, python, biology, genomics, command-line, genbank
Last push: 2026-04-07T06:04:42+00:00

## Health v2 (maintenance only)
Score: 57/100 (v2, computed 2026-09-02T17:46:02.011165+00:00)
- activity 76, release rhythm 8, longevity 100
- inputs: {"age_days": 3774, "days_push": 148, "days_rel": null, "gap_med": null, "n_releases_24m": 0}
- flags: none
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 1083, forks 176 (observed 2026-08-28T04:03:31.181484+00:00)

## What it is
A Python command-line tool for downloading bacterial, fungal, viral, and other genome files from NCBI's FTP servers in GenBank, FASTA, and other formats. It supports filtering by group, section, format, and parallel downloads.

## Use cases
- download all bacterial refseq genomes from ncbi
- fetch fungal genomes in genbank format
- download viral genomes as fasta files
- bulk download genome assemblies for building a kraken database
- mirror ncbi refseq genome data locally
- download genomes in parallel for a bioinformatics pipeline

## When to choose
- you need to bulk-download genomes from NCBI's restructured FTP layout
- you want format, section, and taxonomic group filtering with parallel downloads
- you want a pip or conda (bioconda) installable Python 3 tool

## When to avoid
- you need a GUI or interactive genome browser
- you need to download non-genome NCBI data such as SRA reads or taxonomy dumps
- you are stuck on Python 2 or an unsupported Python version

## Facets
- artifact type: cli-tool
- maturity: active
- function: cli, developer-tools
- domain: bioinformatics
- platform: python, cli, windows, cross-platform
- tags: ncbi, genomics, genome-download, refseq, genbank, bioinformatics, fasta, biology, command-line, data-engineering, linux, macos

## Member repositories
- kblin/ncbi-genome-download (main) score 57

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:03:31.181484+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T06:51:11.294408+00:00, confidence not recorded.
  - readme: https://github.com/kblin/ncbi-genome-download (fetched 2026-08-28T04:03:31.181484+00:00, sha aab72317b1d8)
  - registry_pypi: https://pypi.org/pypi/ncbi-genome-download/json (fetched 2026-08-29T12:53:28.771694+00:00, sha c21e2ca45f26)
- Data as of 2026-08-30T08:39:29.467469+00:00.