nf-core/mag
Version 1

mag

Assembly, binning and annotation of metagenomes.

Build Status Nextflow

install with bioconda Docker

Introduction

This pipeline is for assembly, binning and annotation of metagenomes. It supports both short and long reads, quality trims the reads and adapters with https://github.com/OpenGene/fastp and https://github.com/rrwick/Porechop and performs basic QC with https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

The pipeline then:

Furthermore, the pipeline creates various reports in the results directory specified, including a https://multiqc.info/ report summarizing some of the findings and software versions.

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/mag 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

Credits

This pipeline was written by Hadrien Gourlé at SLU and Daniel Straub (@d4straub).

Long read processing was inspired by caspargross/HybridAssembly written by Caspar Gross @caspargross

help Creators and Submitter
Creator
  • No author provided
Submitter
License
Activity

Views: 226   Downloads: 5

Created: 25th Feb 2020 at 11:09

Last updated: 25th Feb 2020 at 15:19

Last used: 28th Sep 2020 at 08:04

help Attributions

None

help Collections

Related items

Powered by
(v.1.11.master)
Copyright © 2008 - 2020 The University of Manchester and HITS gGmbH