A quick guide for student-driven community genome annotation

TL;DR

This paper presents a scalable, student-driven workflow for manual genome annotation that enhances gene model quality while providing educational opportunities for undergraduates in collaborative research.

Contribution

It introduces a scalable manual annotation workflow involving undergraduates, with quality control, to improve genome annotations and promote scientific education.

Findings

Effective workflow for student-led genome annotation

Improved gene model accuracy through manual curation

Enhanced student engagement in scientific research

Abstract

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.