Workflows

Standardised, reproducible analysis workflows for all major sequencing technologies

Under Development

This web resource is still under active development. Content may be incomplete or subject to change.

Support for selecting, setting up, and running analysis workflows — from pipeline configuration and custom parameterisation to integration into your project.

 

Training · Services

Bulk Sequencing

 

RNA-Seq & miRNA-Seq

PipelineVersion
nf-core/rnaseq3.22.2

 

Immunoglobulin Assembly

Tool
igfinder

 

ChIP-Seq & CUT&RUN

PipelineVersion
nf-core/chipseq2.1.0
nf-core/cutandrun3.2.2

 

ATAC-Seq

PipelineVersion
nf-core/atacseq2.1.2

 

WGS Variant Calling

PipelineVersion
Sarek3.7.1
nf-core/raredisease2.6.0

 

Methyl-Seq

PipelineVersion
nf-core/methylseq4.2.0

 

CRISPR-Seq

PipelineVersion
nf-core/crisprseq2.3.0

Single Cell Sequencing

 

10x Genomics

  • scRNA-seq
  • scATAC-seq
  • Multiome (RNA + ATAC)

 

Variant Calling & Genomic Demultiplexing

Tool
Vireo
Monopogen

 

Parse Biosciences

  • Split-pool combinatorial barcoding scRNA-seq

Long Read Sequencing

 

Nanopore Single Cell

PipelineVersion
nf-core/scnanoseq1.2.1

 

Parse Biosciences Long Read

  • Full-length transcript and isoform-level analysis at single-cell resolution