nf-core

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

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

ATAC-seq peak-calling and QC analysis pipeline

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nanopore demultiplexing, QC and alignment pipeline

Pipeline to fetch metadata and raw FastQ files from public databases

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

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

RNA-seq analysis pipeline for detection of gene-fusions

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

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 of Chromosome Conformation Capture data (Hi-C)

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