Quick start

Summary

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

wget https://github.com/chanzuckerberg/shasta/releases/download/0.1.0/shasta-Linux-0.1.0
chmod ugo+x shasta-Linux-0.1.0
./shasta-Linux-0.1.0 --input input.fasta

Note that the Shasta executable has no dependencies and requires no installation or set up, except for setting its execute permission. See below for more information, including some small changes required for macOS and Windows.

Linux

This will work on most current 64 bit Linux distributions. It was tested on at least the following Linux distributions for the x86_64 architecture, but it is likely that it will run on any Linux distribution for x86_64 that uses a current kernel.

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

Use the Linux directions, but instead download the mac executable with

curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/X.Y.Z/shasta-macOS-X.Y.Z
Make sure to change the name of the executable from shasta-Linux-X.Y.Z to shasta-macOS-X.Y.Z in later steps.

Windows

Quick test and demonstration

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

wget 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
./shasta-Linux-0.1.0 --input r94_ec_rad2.181119.60x-10kb.fasta
This assumes that shasta-Linux-0.1.0 was downloaded to the current directory and made executable as described at the top of this page. 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.