HadrienG / nanoflow

:microscope: De novo assembly of nanopore reads using nextflow
GNU General Public License v3.0
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assembly nanopore nextflow pipeline

Nanoflow

build-status made-with-nextflow gpl

Introduction

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

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

--mem

--assembler

--reads

--output

--fast5

--genome_size

profiles

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

Existing profiles:

License

Code is GPL-3.0

Contributing

We welcome contributions from the community! See our Contributing guidelines