Miniasm

Introduction

Miniasm is a very fast OLC-based de novo assembler for noisy long reads.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/miniasm
Home page: https://github.com/lh3/miniasm

Versions

  • 0.3_r179

Commands

  • miniasm

  • minidot

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 miniasm on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=miniasm
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load miniasm/XXXX ### you can run *module avail miniasm* to check all available versions

miniasm -f Elysia_ont_test.fq  Elysia_reads.paf.gz \
        > Elysia_reads.gfa