nf-core/denovohybrid

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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.