Wtdbg2

Introduction

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT).

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

Versions

  • 2.5

Commands

  • wtdbg-cns

  • wtdbg2

  • wtpoa-cns

Module

You can load the modules by:

module load biocontainers
module load wtdbg

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 Wtdbg2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=wtdbg
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers wtdbg

wtpoa-cns -t 24 -i dbg.ctg.lay.gz -fo dbg.ctg.fa