nf-ginkgo

Nextflow pipeline for Ginkgo (scWGS)

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner.

Ginkgo is a web tool for the analysis of single cell copy number data from whole-genome sequencing data. It was developed mainly by Robert Aboukhalil in Mike Schatz's lab. Further to the web interface, a CLI was made available.

This pipeline runs:

1. FastQC for raw sequencing reads quality control
2. TrimGalore! for adapter trimming
3. bwa to align the reads on the genome
4. samtools for sorting, indexing and getting stats
5. Picard MarkDuplicates, sort, index and BED files
6. BigWigs for display on a browser
7. Ginkgo for the normalisation, segmentation and QC of the single cell libraries
8. MultiQC (does not cover Ginkgo QC)
9. Output Description HTML

Documentation

The nf-ginkgo pipeline is based on the wgsalign pipeline. It comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Running the pipeline
3. Output and how to interpret the results
4. Troubleshooting