nextflow

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

A flexible pipeline for complete analysis of bacterial genomes

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

Nextflow training material

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

Pipeline to fetch metadata and raw FastQ files from public databases

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

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

The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation

RNA-seq analysis pipeline for detection of gene-fusions

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

GATK RNA-Seq Variant Calling in Nextflow