Software: HyPo
Description
HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. It exploits unique genomic kmers to selectively polish segments of contigs using partial order alignment of selective read-segments.
Available Versions
| Unspecified: | 1.0.3 |
|---|
As demonstrated on human genome assemblies, Hypo generates significantly more accurate polished assembly in about one-third time with about half the memory requirements in comparison to contemporary widely used polishers like Racon.
BioContainers: https://biocontainers.pro/tools/hypo
Home page: https://github.com/kensung-lab/hypo
Commands
- hypo
Module
You can load the modules by:
module load biocontainers
module load hypo
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 hypo on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hypo
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers hypo