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Quick start

Note that the Shasta executable has no dependencies and requires no installation or set up. This means that you can use it immediately afterdownloading it and setting its execute permission. See below for more information.

Linux

You can use the following commands to download the executable from the latest release and run an assembly: 

# Download the executable for the latest release.
curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.10.0/shasta-Linux-0.10.0

# Grant execute permissions.
chmod ugo+x shasta-Linux-0.10.0

# Run an assembly.
./shasta-Linux-0.10.0 --input input.fasta --config Nanopore-May2022

You can specify multiple input FASTA files, if necessary. On a typical laptop, this will run in minutes for a bacterial genome. For a human size assembly, AWS instance type x1.32xlarge is recommended. It is usually available at a cost around $4/hour on the AWS spot market and should complete the human size assembly in a few hours, at coverage around 60x.

Assembly output will be created in a new directory named ShastaRun. Output includes the assembly in FASTA and GFA 1.0 formats in files:

This will work on all current 64 bit Linux distributions that use Linux kernel 3.2.0 or newer.

Note that the procedure above does not require root privilege, unless some non-default options are used when invoking the executable. Those non-default options are, however, necessary to achieve maximum performance.

macOS

If you are on a macOS system with Intel processors, you can use the following commands to get started: 

# Download the executable for the latest release.
curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.10.0/shasta-macOS-11-Intel-0.10.0

# Grant necessary permissions.
chmod ugo+x shasta-macOS-11-Intel-0.10.0

# Run an assembly.
./shasta-macOS-11-Intel-0.10.0 --input input.fasta --config Nanopore-May2022
If you are on a macOS system with Apple ARM processors, use the same commands, changing the name of the executable to shasta-macOS-11-ARM-0.10.0.

Windows


Quick test and demonstration

You can use the following commands to run a quick test and demonstration of the Shasta assembler: 

curl -O -L https://s3-us-west-2.amazonaws.com/lc2019/shasta/ecoli_test/r94_ec_rad2.181119.60x-10kb.fasta.gz
gunzip r94_ec_rad2.181119.60x-10kb.fasta.gz
/path/to/shasta_executable --input r94_ec_rad2.181119.60x-10kb.fasta --config Nanopore-May2022
The first two commands download and decompress an input fasta file containing Oxford Nanopore reads for E. coli. The last command runs a Shasta assembly, which should complete in a few minutes on a laptop with at least 8 GB of memory. Assembly output will appear in a new directory ShastaRun. See in particular ShastaRun/Assembly.fasta and ShastaRun/Assembly.gfa.

For more information

More detailed information on running an assembly is available here. A list of command line options can be found here.

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