ERGA is an international consortium of over 700 researchers from across Europe who are committed to cataloguing eukaryotic biodiversity through the generation of high-quality reference genomes as a response to biodiversity declines. Development and implementation of standard procedures and bioinformatic pipelines is essential for achieving ERGA’s goal.
Annotation of reference genomes is necessary for many downstream analyses, but tools and workflows for genome annotation are still not ready to scale up. However, as the number of sequenced genomes is rapidly increasing, there is a great need to develop standard, efficient and reproducible genome annotation workflows. In this project we will develop and implement pipelines for performing and evaluating genome annotations. For this, we will identify appropriate pipeline components, create environments or containers to facilitate their installation (if necessary) and embed them into robust pipelines using a standard workflow manager such as Snakemake.
We need people interested in genome annotation and with basic experience either in genome annotation; pipeline development or tool packaging.
In order to achieve all the objectives stated in our proposal, we would like to divide the workload in at least three subgroups:
- Coordination, documentation and workflow release
- Genome annotation
- Evaluation of genome annotations
Our short-term objectives will be to identify the tools that will become pipeline components and make them accessible via Conda or containers. Next, we will need to wrap them up into reproducible and robust pipelines. Importantly, we will daily document and release each of the achievements.
Long-term goals will be to finish and release all the developed pipelines, finish the Biohackrxiv paper and run the pipelines on any ERGA assembled genomes. There is currently an absence of such general tools for annotation, so we anticipate that this tool would be widely adopted.
We need people interested in genome annotation and with basic experience either in genome annotation; pipeline development (I.e. with Snakemake) or tool packaging.
Jèssica Gómez Garrido, Alice B. Dennis