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