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

A curated collection of Nextflow implementation patterns

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

Assembly and binning of metagenomes

A single-cell RNAseq pipeline for 10X genomics data

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

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

RNA-seq analysis pipeline for detection of gene-fusions

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

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

GATK RNA-Seq Variant Calling in Nextflow

Nextflow training material

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

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