The hybrid-assembly pipeline contains workflows for de-novo genome assembly using both short and long reads. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The current workflow consists of:
- Quality control of input reads
- Assembly
- Assesment of assembly quality
Three different assemblers are currently implemented:
The hybrid-assembly pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
This pipeline was written by Kevin Menden (kevinmenden) at DZNE.
