longread-polish-nf

Nextflow pipeline for polishing an assembly with long reads and racon

Introduction

Polishing a genome assembly with racon is pretty simple, except that it can take a while on large genomes and so you might want to distribute the tasks into one job per contig/scaffold/chromosome on a cluster. This pipeline does that distribution for you.

Requirements

Data

• Long reads
• An assembly created from those long reads

Nextflow

• nextflow — can be installed with the command curl -s https://get.nextflow.io | bash

Other software

• racon
• minimap2
• samtools

This pipeline is set up to use mamba to create an environment with these three programs in it, but you can always install them yourself or use modules. See configuration section below.

Configuration

Nextflow configuration is handled by the file nextflow.config in the directory where you're running the nextflow command. The configuration file in this repository is for running the pipeline on the lewis cluster at Mizzou using SLURM and mamba, but you can adjust it to use any batch or cloud system you want. Check out the nextflow docs for more information.

If you don't have a conda environment already set up with racon, minimap2, and samtools installed in it, you can have nextflow make one for you by changing the conda line of the config to

conda = "racon minimap2 samtools"

Lewis-specific stuff

Nextflow needs a filesystem where locking is allowed for keeping track of which jobs are running, but not to actually store the data or temporary files you're creating. On Lewis, HTC allows locking but is slow and HPC does not allow locking but is fast. To take advantage of the best of both worlds, run this pipeline from within a project directory in HTC, but set the environment variable $NXF_WORK to point to an empty directory on HPC.

Running

To download the pipeline and run it on your assembly, just run the command:

nextflow run WarrenLab/longread-polish-nf \
    --reference unpolished_assembly.fa \
    --reads 'long_reads/*.fastq.gz'

This will align all the reads to your reference and then use the alignments to correct the assembly.

N.B. The single quotes around the --reads parameter are necessary to keep bash from expanding the asterisk; we want nextflow to do that expansion.

TODO

• Write help message
• Convert to DSL2
• Add option for ONT reads