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

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

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nextflow training material

Pipeline to fetch metadata and raw FastQ files from public databases

RNA-seq analysis pipeline for detection of gene-fusions

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

Nextflow pipeline to analyze PacBio HiFi full-length 16S data

Precision HLA typing from next-generation sequencing data

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

A bioinformatics pipeline to phase and impute genetic data

nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

nf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

16S RNA microbiome pipeline