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ikmb-denbi / genome-annotation

A nextflow pipeline with automatic software provisioning to generate hints and subsequent genome model predictions with AUGUSTUS
MIT License
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!!! THIS PROJECT HAS BEEN RETIRED. PLEASE WORK WITH ITS DROP-IN REPLACEMENT: https://github.com/ikmb/esga

ESGA - Genome Annotation

Nextflow install with bioconda Singularity Container available

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.