bcbio/bcbio-nextgen

Health v2 · maintenance only

Adoption not part of the score

1030 stars · 355 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

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

application · maturity abandoned

workflow-automation etl data-science bioinformatics python cloud cli genomics variant-calling rna-seq sequencing-pipelines high-throughput discontinued data-engineering automation linux docker

Member repositories

For agents

markdown · JSON · MCP: product_card(name="bcbio/bcbio-nextgen")