Pipelines

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

Assembly and binning of metagenomes

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

A single-cell RNAseq pipeline for 10X genomics data

ATAC-seq peak-calling and QC analysis pipeline

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nanopore demultiplexing, QC and alignment pipeline

RNA-seq analysis pipeline for detection of gene-fusions

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

Pipeline to fetch metadata and raw FastQ files from public databases

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

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

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

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

A small-RNA sequencing analysis pipeline

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.