RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Repository to host tool-specific module files for the Nextflow DSL2 community!

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Python package with helper tools for the nf-core community.

Assembly and binning of metagenomes

Amplicon sequencing analysis workflow using DADA2 and QIIME2

ChIP-seq peak-calling, QC and differential analysis pipeline.

Nanopore demultiplexing, QC and alignment pipeline

ATAC-seq peak-calling and QC analysis pipeline

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair

Pipeline to fetch metadata and raw FastQ files from public databases

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

RNA-seq analysis pipeline for detection of gene-fusions

Assembly and intrahost/low-frequency variant calling for viral samples

Test data to be used for automated testing with the nf-core pipelines

Call and score variants from WGS/WES of rare disease patients.

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

Config files used to define parameters specific to compute environments at different Institutions

Analysis of Chromosome Conformation Capture data (Hi-C)

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

(Meta-)genome screening for functional and natural product gene sequences

Protein 3D structure prediction pipeline

A small-RNA sequencing analysis pipeline

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

A single cell transcriptomics pipeline for QC, integration and making the data presentable

Code and files for the main nf-core website.

Simple bacterial assembly and annotation pipeline