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<h1>Shasta long read assembler</h1>
<p>
This is the documentation for the
<a href="https://github.com/paoloshasta/shasta">
Shasta long read assembler</a>.
If you are seeing this documentation on <code>github.io</code>,
it applies to the latest version of Shasta
on GitHub (not necessarily the same as the latest release).
Documentation for any version of Shasta is available
in the source code in the <code>shasta/docs</code> directory
and in any build under the <code>shasta-build/shasta-install/docs</code>
directory.
</p>
<h3>Abstract</h3>
<p>
The goal of Shasta is to rapidly
produce accurate assembled sequence using as input DNA reads
generated by <a href="https://nanoporetech.com">Oxford Nanopore</a> flow cells.
</p>
<p>
Computational methods used by the Shasta assembler include:
<ul>
<li>
Using a
<a href='https://en.wikipedia.org/wiki/Run-length_encoding'>run-length</a>
representation of the read sequence.
This makes the assembly process more resilient to errors in
homopolymer repeat counts, which are the most common type
of errors in Oxford Nanopore reads.
<li>
Using in some phases of the computation a representation
of the read sequence based on <i>markers</i>, a fixed
subset of short k-mers (k ≈ 10).
</ul>
</p>
<p>
An current implementation of Shasta is complete and functional,
but significant improvements in several areas are possible.
As implemented, it can run an assembly of a human genome at coverage around 60x
in about 5 hours using a single, large machine (AWS instance type
<code>x1.32xlarge</code>, with 128 virtual processors and 1952 GB of memory).
The compute cost of such an assembly is around $20 at AWS spot market or reserved prices.
</p>
<p style="font-style:italic;">
See <a href='https://www.nature.com/articles/s41587-020-0503-6'>Shafin et al, Nature Biotechnology 2020</a>
for an error analysis of the Shasta assembler and more.
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