nanoflow
nanoflow copied to clipboard
:microscope: De novo assembly of nanopore reads using nextflow
Nanoflow
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 | ✔️ | |
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