Nanoflow

Introduction

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		✔️
assembly	miniasm + minimap2	0.2-r168 / 2.10-r768		✔️
	canu	Unknown		✔️
	unicycler	0.4.5		✔️
consensus	racon + minimap2	1.3.1 / 2.10-r768		✔️
polishing	nanopolish	Unknown		✔️

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