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 containers making installation trivial and results highly reproducible.


The nf-core/denovohybrid pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
    * Local installation
    * Adding your own system config
    * Reference genomes
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

The *Denovohybrid* pipeline allows the generation of high quality genome assemblies using a combination of long read data (Oxford Nanopore Technologies) and short read data (Illumina Technologies). It includes read preprocessing and quality control, a choice of different assembly methods and quality control of the resulting assemblies. Depending on the assembly method it can be used for Bacteria (using *Unicycler*) or Eukaryotic samples (using *miniasm* or *wtdbg2*). When no short read data is provided, this pipeline automatically creates a long read only assembly.


* Check out new long read assemblers:
* Shasta
* wengan
* wait for flye to be available in python3


nf-core/denovohybrid was originally written by Caspar Groß.