Shasta Documentation
- Introduction
- Quick start
- Command line options
- 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
- 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
- High performance computing techniques
- Compatibility across releases
- Acknowledgments