DOI: 10.12688/f1000research.191681.1 ISSN: 2046-1402

The Genome Lab: designing a simpler interface for genome assembly and annotation

Anna Syme, Cameron Hyde, W.C. Mike Thang, Winnie Mok, Gareth Price
Show PDF Cite
Background Galaxy is a web-based platform for analysing data, particularly biological data such as DNA. While genome assembly and annotation is a typical starting point for users, navigating this process can be challenging: many factors affect which tools and settings are appropriate, and researchers with genomes to analyse often have deep taxonomic expertise but less bioinformatics experience. Methods To better present relevant resources, we built the Genome Lab: a domain-specific interface for genome assembly and annotation. Informed by user experience considerations, the design targets discoverability and navigation, and is intended to reduce the effort required to find resources and to understand the genome assembly process. Applying six key design decisions, we gave the Lab a clear, simple layout showing an organised set of tools and workflows, so that new users can get started quickly and experienced users have their frequently required resources at hand. Results We present a worked example of genome assembly and annotation, carried out the way a researcher might use the Genome Lab. Working from Nanopore sequencing reads, the curated path produced a genome assembly, a completeness assessment and gene models, viewed in a genome browser. Conclusions The Genome Lab has been implemented as a generic framework that other communities have since used to build Labs for their own domains, on Galaxy Australia and elsewhere. A curated, domain-specific interface provides a simpler entry point for researchers new to the field. We describe the design decisions, the framework and a worked example, which may help other groups build a similar interface for their own domain.

More from our Archive