This pipeline can be used to generate "hints" from aligned sequence evidence to annotate a genome de novo.
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Hints file is generated from all available evidences (proteins, EST and/or RNA-seq reads).
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Gene models are predicted using Augustus with the hints file as extrinsic evidence (optional).
The minimum requirements are a genome file and at least one type of evidence.
A simple test data set can be downloaded here
Documentation about the pipeline can be found in the docs/
directory or under the links below:
- What happens in this pipeline?
- Recommendations
- Installation and configuration
- Running the pipeline
- Output
- Troubleshooting
- What's next
This pipeline was written by Dr. Montserrat Torres (MontseTor) and Dr. Marc Höppner (marchoeppner) at IKMB. The authors gratefully acknowledge inspiration, fruitful discussions and a few useful code snippets from the nf-core.