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Hifiasm

Introduction

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads.

For more information, please check its website: https://biocontainers.pro/tools/hifiasm and its home page on Github.

Versions

  • 0.16.0
  • 0.18.5

Commands

  • hifiasm

Module

You can load the modules by:

module load biocontainers
module load hifiasm

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 Hifiasm on our clusters:

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

module --force purge
ml biocontainers hifiasm