Bioinformatics Pipeline
1.3k 2026-04-18
nf-core/rnaseq
A robust Nextflow pipeline for comprehensive RNA sequencing data analysis, offering quality control, alignment, and gene/isoform quantification.
Core Features
Comprehensive RNA-seq analysis including QC, trimming, alignment, and quantification.
Supports multiple aligners and quantifiers like STAR, RSEM, HISAT2, and Salmon.
Generates gene and isoform expression matrices along with extensive quality control reports.
Includes advanced features such as UMI extraction, deduplication, and contaminant removal.
Flexible input handling for both raw FASTQ files and pre-aligned BAM files.
Detailed Introduction
nf-core/rnaseq is a standardized bioinformatics pipeline designed for analyzing RNA sequencing data from organisms with a reference genome and annotation. It streamlines the complex process from raw FASTQ or pre-aligned BAM files through quality control, adapter trimming, contaminant removal, and alignment using tools like STAR, HISAT2, or Salmon. The pipeline generates accurate gene and isoform counts, alongside comprehensive quality control reports, ensuring reproducible and high-quality results for gene expression studies within a Nextflow framework.