Marginpolish

Introduction

MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.

For more information, please check:

Docker hub: https://hub.docker.com/r/kishwars/margin_polish

Home page: https://github.com/UCSC-nanopore-cgl/MarginPolish

Versions

• 0.1.3

Commands

• marginpolish

Module

You can load the modules by:

module load biocontainers
module load marginpolish

Example job

Warning

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 marginpolish on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 32
#SBATCH --job-name=marginpolish
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers marginpolish

marginpolish \
    Reads_to_assembly_StaphAur.bam \
    Draft_assembly_StaphAur.fasta \
    helen_modles/MP_r941_guppy344_microbial.json \
    -t 32 \
    -o mp_output/mp_images \
    -f