Shasta

Overview

Shasta is a de novo genome assembly software that uses nanopore reads.

Version 0.8.0 is available.

Restrictions on use

Shasta is free to use software, users can familiarise themselves with the license information before using it.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load the modulefile corresponding to your required version:

module load apps/binapps/shasta/0.8.0

Running the application

We recommend to run Shasta by submitting a parallel job. Be sure to have the input file in your working directory.

#!/bin/bash --login
#$ -cwd			# Job will run from the current directory
#$ -pe smp.pe 8		# Number of cores (2-32 permitted)

# Load the modulefile in the jobscript (hence --login on first line, and no -V flag)
module load apps/binapps/shasta/0.8.0

# Run in 'local' mode (turn off Grid, and indicate max number of threads and memory)
/bin/date
shasta-Linux-0.8.0 --input test_J1.fastq --config Nanopore-Oct2021
/bin/date
echo end

Further info

More info on commands, functions and getting started may be found here:
https://chanzuckerberg.github.io/shasta/