Nextflow pipeline for Ginkgo (scWGS)
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:
- FastQC for raw sequencing reads quality control
- TrimGalore! for adapter trimming
- bwa to align the reads on the genome
- samtools for sorting, indexing and getting stats
- Picard MarkDuplicates, sort, index and BED files
- BigWigs for display on a browser
- Ginkgo for the normalisation, segmentation and QC of the single cell libraries
- MultiQC (does not cover Ginkgo QC)
- Output Description HTML
The nf-ginkgo pipeline is based on the wgsalign pipeline. It comes with documentation about the pipeline, found in the docs/ directory: