Version 1

Workflow Type: Nextflow


Hybrid genome assembly.

Build Status Nextflow

install with bioconda Docker


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
  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:


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

Version History

Version 1 (earliest) Created 25th Feb 2020 at 11:04 by Finn Bacall

Added/updated 25 files

Open master a586631
help Creators and Submitter
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Additional credit

Caspar Gross


Views: 1152   Downloads: 29

Created: 25th Feb 2020 at 11:04

Last updated: 25th Feb 2020 at 15:19

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