## Shasta Documentation

🆕 Mode 3 assembly: presentation of assembly results

🆕 Mode 3 assembly: usage notes

If you are looking at this documentation on GitHub Pages (`https://paoloshasta.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

- On Linux
- On macOS
- On Windows
- Test/Demo

- 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
- Dealing with errors

- Mode 3 assembly: usage notes
- Exploring assembly results
- Maximizing assembly performance
- Shasta commands
- Building from source
- 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