nf-core/rnaseq

Health v2 · maintenance only

Adoption not part of the score

1357 stars · 891 forks observed · 2026-08-28

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

nf-core/rnaseq is a Nextflow-based bioinformatics pipeline for analyzing RNA sequencing data, performing QC, trimming, (pseudo-)alignment with STAR, HISAT2, or Salmon, and producing gene/isoform count matrices with extensive QC reporting. It runs with Docker, Singularity, or Conda and is part of the nf-core community pipeline collection.

Use cases

• analyze RNA-seq FASTQ files and get gene counts
• run a reproducible RNA sequencing pipeline
• align RNA-seq reads with STAR or HISAT2
• quantify transcript expression with Salmon or RSEM
• generate MultiQC quality reports for RNA-seq data
• process bulk RNA-seq samples at scale on HPC or cloud
• reprocess BAM files to regenerate expression matrices

When to choose

• you need a community-maintained, best-practice RNA-seq analysis workflow
• you want reproducible results with containerized software on HPC or cloud
• you need extensive QC reporting and multiple alignment/quantification options
• you have a reference genome and annotation for your organism

When to avoid

• you lack a reference genome (de novo transcriptome assembly is out of scope)
• you need single-cell RNA-seq analysis (use nf-core/scrnaseq instead)
• you want a lightweight one-off alignment without a full pipeline
• you cannot install Nextflow or a container runtime

Facets

application · maturity active

workflow-automation etl data-science analytics bioinformatics cloud cli self-hosted nextflow nf-core rna-seq bioinformatics-pipeline star salmon hisat2 rsem quality-control multiqc genomics transcriptomics fastq alignment gene-expression data-engineering automation linux macos docker

Member repositories

For agents

markdown · JSON · MCP: product_card(name="nf-core/rnaseq")