New Shasta Documentation
The current Shasta documentation is available here.
The rest of this page contains documentation for an old and obsolete Shasta repository. The new and current Shasta repository is here. For more information about the transition in Shasta repositories, see the README file here.
Old Shasta Documentation
If you are looking at this documentation on GitHub Pages
(https://chanzuckerberg.github.io/shasta/),
this documentation applies to the latest Shasta code on GitHub
and might contain features that are not available in the Shasta version
you are using.
To obtain documentation that applies to a specific release,
download the tar file for that release
and, after extracting it, look at index.html
in the docs directory.
- Introduction
- Quick start
- Command line options
- Assembly configurations
- Supported platforms
- Running an assembly
- Selecting assembly options
- Memory requirements
- Running with less than optimal memory
- Memory modes
- Scripting with Python
- Running an assembly in Docker
- Dealing with errors
- Exploring assembly results
- Maximizing assembly performance
- Shasta commands
- Building from source
- Contributing to Shasta
- Reporting problems or asking questions
- Computational methods
- Long reads
- Computational challenges
- Read representation
- Run-length encoding
- Markers
- Marker alignments
- Finding overlapping reads
- Initial assembly steps
- Read graph
- Marker graph
- Assembly graph
- Using the marker graph to assemble sequence
- Assembling repeat counts
- Selecting assembly paths
- Detangling
- Iterative assembly
- Phased diploid assembly
- High performance computing techniques
- Compatibility across releases
- Acknowledgments