# bcbio/bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Repository: https://github.com/bcbio/bcbio-nextgen
Canonical: https://ross.abutalabs.com/products/bcbio-nextgen
Homepage: https://bcbio-nextgen.readthedocs.io
Language: Python
License: MIT
License Family: permissive
Last push: 2024-08-24T11:11:30+00:00

## Health v2 (maintenance only)
Score: 23/100 (v2, computed 2026-09-02T17:46:02.011165+00:00)
- activity 0, release rhythm 8, longevity 100
- inputs: {"age_days": 4956, "days_push": 739, "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 1030, forks 355 (observed 2026-08-28T04:03:17.893113+00:00)

## What it is
bcbio-nextgen is a validated, community-developed pipeline toolkit for high-throughput sequencing analysis, including variant calling, RNA-seq, and small RNA workflows. Users write a high-level configuration file that drives distributed, idempotent, transactional parallel execution across multicore machines, clusters, or the cloud.

## Use cases
- call variants from whole genome sequencing data
- run RNA-seq differential expression pipelines
- analyze small RNA sequencing data
- scale sequencing analysis across a compute cluster
- validate variant calls against reference materials
- run single-cell RNA-seq analysis pipelines

## When to choose
- you need validated, best-practice genomics pipelines with automated validation against reference materials
- you need to scale whole genome or population-level sequencing analysis across clusters or the cloud
- you want a single config-driven pipeline covering variant calling, RNA-seq, and small RNA analysis

## When to avoid
- the project was officially discontinued in August 2024, so new features and fixes should not be expected
- you need actively maintained tooling for production pipelines
- you need a lightweight single-purpose tool rather than a full pipeline framework

## Facets
- artifact type: application
- maturity: abandoned
- function: workflow-automation, etl, data-science
- domain: bioinformatics
- platform: python, cloud, cli
- tags: genomics, variant-calling, rna-seq, sequencing-pipelines, high-throughput, discontinued, data-engineering, automation, linux, docker

## Member repositories
- bcbio/bcbio-nextgen (main) score 23

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:03:17.893113+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 2026-08-30T07:07:32.483691+00:00, confidence not recorded.
  - readme: https://github.com/bcbio/bcbio-nextgen (fetched 2026-08-28T04:03:17.893113+00:00, sha b41dc2642b26)
  - registry_pypi: https://pypi.org/pypi/bcbio-nextgen/json (fetched 2026-08-29T13:07:48.758567+00:00, sha 2aada8b30b10)
- Data as of 2026-08-30T08:39:29.467469+00:00.