RCAC - Software: Homopolish

Software: Homopolish

Type

Resource

Description

Homopolish is a genome polisher originally developed for Nanopore and subsequently extended for PacBio CLR. It generates a high-quality genome (>Q50) for virus, bacteria, and fungus. Nanopore/PacBio systematic errors are corrected by retreiving homologs from closely-related genomes and polished by an SVM.

Available Versions

Available Versions
Unspecified:	0.4.1

When paired with Racon and Medaka, the genome quality can reach Q50-90 (>99.999%) on Nanopore R9.4/10.3 flowcells (Guppy >3.4). For PacBio CLR, Homopolish also improves the majority of Flye-assembled genomes to Q90.

Docker hub: https://hub.docker.com/r/staphb/homopolish
Home page: https://github.com/ythuang0522/homopolish

Commands

homopolish

Module

You can load the modules by:

module load biocontainers
module load homopolish

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run homopolish on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=homopolish
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers homopolish