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.
- Download the Linux static executable
shasta-Linux-X.Y.Zfor your selected release. You can use your browser or the following command, replacing
X.Y.Zwith the release you want to use:
- Use this command to set its permission bits:
chmod ugo+x shasta-Linux-X.Y.Z
- Use this command to run your assembly, making sure to specify
the correct path to the location where you stored the executable,
or to add that location to your
./shasta-Linux-X.Y.Z --input input.fastaYou 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
x1.32xlargeis 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:
x86_64architecture, but it is likely that it will run on any Linux distribution for
x86_64that uses a current kernel.
- Ubuntu 16.04 and 18.04
- Linux Mint 18.3
- CentOS 7.6
- Debian 9
- Fedora 29
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.
macOSUse the Linux directions, but instead download the mac executable with
Make sure to change the name of the executable from
curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/X.Y.Z/shasta-macOS-X.Y.Z
shasta-macOS-X.Y.Zin later steps.
- Install Windows Subsystem for Linux (WSL).
- Working in a Linux shell created using WSL, follow the directions for Linux above.
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.fastaThis assumes that
shasta-Linux-0.1.0was 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
For more information
More detailed information on running an assembly is available here. A list of command line options can be found here.