Software: MarginPolish
Description
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.
Available Versions
| Unspecified: | 0.1.3 |
|---|
Docker hub: https://hub.docker.com/r/kishwars/margin_polish
Home page: https://github.com/UCSC-nanopore-cgl/MarginPolish
Commands
- marginpolish
Module
You can load the modules by:
module load biocontainers
module load marginpolish
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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