shasta
Link to section 'Introduction' of 'shasta' Introduction
Shasta is a software for de novo assembly from Oxford Nanopore reads.
Home page: https://github.com/chanzuckerberg/shasta
Link to section 'Versions' of 'shasta' Versions
- 0.10.0
Link to section 'Commands' of 'shasta' Commands
- shasta
Link to section 'Module' of 'shasta' Module
You can load the modules by:
module load biocontainers
module load shasta
Link to section 'Example job' of 'shasta' Example job
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