Shasta

Introduction

Shasta is a software for de novo assembly from Oxford Nanopore reads.

For more information, please check:

Home page: https://github.com/chanzuckerberg/shasta

Versions

0.10.0

Commands

shasta

Module

You can load the modules by:

module load biocontainers
module load shasta

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 shasta on our clusters:

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

module --force purge
ml biocontainers shasta

shasta --input r94_ec_rad2.181119.60x-10kb.fasta \
    --config Nanopore-May2022