mhoeppner/genome-annotation repository overview

⁠ESGA - Genome Annotation

This pipeline can be used to generate "hints" from aligned sequence evidence to annotate a genome de novo.

⁠Pipeline main steps

1. Hints file is generated from all available evidences (proteins, EST and/or RNA-seq reads).

2. 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.

⁠Test data

A simple test data set can be downloaded here⁠

⁠Documentation

Documentation about the pipeline can be found in the docs/ directory or under the links below:

1. What happens in this pipeline?⁠
2. Recommendations⁠
3. Installation and configuration⁠
4. Running the pipeline⁠
5. Output⁠
6. Troubleshooting⁠
7. What's next⁠

⁠Pipeline Scheme

⁠Credits

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.