nf-core/denovohybrid

Edit

Introduction

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.

Documentation

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.

*Todos:*

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

Credits

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