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

A flexible pipeline for complete analysis of bacterial genomes

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!

A curated collection of Nextflow implementation patterns

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

Assembly and binning of metagenomes

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

ATAC-seq peak-calling and QC analysis pipeline

Nanopore demultiplexing, QC and alignment pipeline

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Pipeline to fetch metadata and raw FastQ files from public databases

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

Nextflow training material

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

GATK RNA-Seq Variant Calling in Nextflow

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

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing