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<h1>Quick start</h1>
Note that the Shasta executable has no dependencies and requires no installation
or set up. This means that you can use it immediately after downloading it and setting its execute permission.
See below for more information.
<h2 id="QuickStartLinux">Linux</h2>
<p>
You can use the following commands to download the executable from the latest release and run an assembly:
<pre>
# Download the executable for the latest release.
curl -O -L https://github.com/paoloshasta/shasta/releases/download/0.11.1/shasta-Linux-0.11.1
# Grant execute permissions.
chmod ugo+x shasta-Linux-0.11.1
# Run an assembly.
./shasta-Linux-0.11.1 --input input.fasta --config Nanopore-May2022
</pre>
<p>
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 <code>x1.32xlarge</code>
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.
<p>
Assembly output will be created in a new directory named
<code>ShastaRun</code>.
Output includes the assembly in FASTA and GFA 1.0 formats in files:
<ul>
<li><code>ShastaRun/Assembly.fasta</code>
<li><code>ShastaRun/Assembly.gfa</code>
<li><code>ShastaRun/Assembly-BothStrands.gfa</code>
</ul>
This will work on all current 64 bit Linux distributions
that use Linux kernel 3.2.0 or newer.
</ul>
<p>
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.
<h2 id="QuickStartWindows">Windows</h2>
<ul>
<li>
Install
<a href="https://docs.microsoft.com/en-us/windows/wsl/install-win10">
Windows Subsystem for Linux (WSL)</a>.
<li>Working in a Linux shell created using WSL, follow the directions for Linux above.
</ul>
<br/>
<h2 id=QuickDemo>Quick test and demonstration</h2>
<p>
You can use the following commands to run a quick test and demonstration
of the Shasta assembler:
<pre>
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
</pre>
The first two commands download and decompress an input fasta file
containing Oxford Nanopore reads for <i>E. coli</i>.
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 <code>ShastaRun</code>. See in particular
<code>ShastaRun/Assembly.fasta</code> and
<code>ShastaRun/Assembly.gfa</code>.
<h2>For more information</h2>
<p>
More detailed information on running an assembly is available
<a href=Running.html>here</a>.
A list of command line options can be found
<a href=CommandLineOptions.html>here</a>.
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