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

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.

Amplicon sequencing analysis workflow using DADA2 and QIIME2

ATAC-seq peak-calling and QC analysis pipeline

Nanopore demultiplexing, QC and alignment 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 or bwa-meth + MethylDackel

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

RNA-seq analysis pipeline for detection of gene-fusions

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

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

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Analysis of Chromosome Conformation Capture data (Hi-C)

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

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.