Shasta long read assembler

This is the documentation for the Shasta long read assembler. If you are seeing this documentation on github.io, it applies to the latest version of the Shasta assembler on GitHub (not necessarily the same as the latest release). Documentation for any version of Shasta is available in the source code in the shasta/docs directory and in any build under the shasta-build/shasta-install/docs directory.

Abstract

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

Computational methods used by the Shasta assembler include:

An initial implementation of the Shasta assembler is complete and functional, but significant improvements in several areas are possible. As currently 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 x1.32xlarge, 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.

The accuracy of assembled sequence is being analyzed. Early indications are that Shasta is similar or better in assembly quality when compared to other long read assemblers.

Quick start

Command line options

Motivation

Current status

Supported platforms

How to:

Acknowledgments

Computational methods

Compatibility across releases