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For information on how to prepare your data to run the full analysis with Transposome, take a look at the Quick Start page. If you are interested in using Transposome to create your own analysis pipelines, see the API Tutorial section, which contains numerous examples. If you are having problems getting Transposome to compile or run, see the Troubleshooting page. For advanced users, you can contact me if you are interested in extending or modifying Transposome or just fork the repo and modify things to your needs.

Basic usage (start here if you have Transposome installed)

• Quick Start

Installation and troubleshooting

• Installing dependencies
• Troubleshooting

Documentation of file formats used or generated by Transposome

• File specifications (description of input/output formats) and example usage
• Preparing sequence data for Transposome

Advanced usage, including the design of custom annotation pipelines

• API Tutorial
• Running individual analysis steps