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🔬 De novo assembly of nanopore reads using nextflow

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Nanoflow

build-status made-with-nextflow gpl

Introduction

⚠️ This repository is deprecated. Please use https://github.com/nf-core/bacass instead ⚠️

Nanoflow aims at being a reproducible pipeline for bacterial genome assembly of nanopore reads.

Nanoflow uses the following software

Task Software Version Docker Lmod + SGE
adapter trimming porechop 0.2.3 Docker Build Status ✔️
assembly miniasm + minimap2 0.2-r168 / 2.10-r768 Docker Build Status ✔️
canu Unknown Docker Build Status ✔️
unicycler 0.4.5 Docker Build Status ✔️
consensus racon + minimap2 1.3.1 / 2.10-r768 Docker Build Status ✔️
polishing nanopolish Unknown Docker Build Status ✔️

Installation

To install nextflow (make sure you have java installed):

curl -fsSL get.nextflow.io | bash

You'll also need docker installed if you wish to run the pipeline locally.

Usage

Once you have nextflow and docker installed:

nextflow run hadrieng/nanoflow --reads reads.fasta --assembler unicycler --output results

Options

--cpus

  • number of cpus
  • 4 by default

--mem

  • amount of memory to use, in GB
  • 8GB by default
  • has to end with "GB"

--assembler

  • which assembler to use
  • can be miniasm, unicycler or canu
  • required

--reads

  • location of the nanopore reads in fasta or fastq
  • required

--output

  • output directory
  • required

--fast5

  • location of the fast5 files
  • required for polishing with nanopolish

--genome_size

  • genome size of the organism you are trying to assemble
  • required if --assembler canu

profiles

By default nanoflow will execute on your local nachine using dockers. You can modify this behavior with the -profile option

Existing profiles:

  • planet: to execute it on the SGBC cluster

License

Code is GPL-3.0

Contributing

We welcome contributions from the community! See our Contributing guidelines

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