Quick start
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
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/0.7.0/shasta-Linux-0.7.0 # Grant necessary permissions. chmod ugo+x shasta-Linux-0.7.0 # Run an assembly. ./shasta-Linux-0.7.0 --input input.fasta
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:
ShastaRun/Assembly.fasta
ShastaRun/Assembly.gfa
ShastaRun/Assembly-BothStrands.gfa
x86_64
architecture.
- Ubuntu 16.04 LTS
- Ubuntu 18.04 LTS
- Ubuntu 20.04 LTS
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
# Download the executable for the latest release. curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.7.0/shasta-macOS-0.7.0 # Grant necessary permissions. chmod ugo+x shasta-macOS-0.7.0 # Run an assembly. ./shasta-macOS-0.7.0 --input input.fastaThe macOS executable has been tested on macOS 10.15 (Catalina) and macOS 10.14 (Mojave).
Windows
- 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:
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.fastaThe 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.