Deep learning meets genome annotation: rapid gene prediction tool now available
The deep learning-based genome annotation tool, Tiberius, is now available in Galaxy Australia. After being wrapped and extensively tested, it is freely available for everyone’s use in the Genome Lab.
Tiberius offers gene structure prediction from genomic sequences alone (ab initio). With accuracy that matches tools using extrinsic data, it provides end-to-end prediction of protein-coding genes. Tiberius can be installed and run by individuals, and also parallelised on HPC systems. But now that the wrapper is available in the Galaxy toolshed, it can easily be used by Australian researchers in the Galaxy Australia platform (or installed on any other international Galaxy instance). Tiberius has been trained on organisms in Bacillariophyta, Chlorophyta, Fungi, Insecta, Mammalia, Mesangiospermae, and Vertebrata, and all of those models are available on Galaxy.
Image: Getty Images via Canva
During an internship with the Australian Tree of Life Bioinformatics team, University of Queensland PhD candidate, Jane Tung, did much of the initial work to get Tiberius up and running. She benchmarked the performance of three traditional and two machine learning-based eukaryotic genome annotation pipelines using datasets spanning fungi, plants, insects, fish, lizards, amphibians, birds and mammals. Tiberius completed the annotation in a fraction of the time and used fewer resources compared to the traditional pipelines, without a negative effect on quality metrics. Jane will be discussing these findings further in November via the webinar Benchmarking the latest annotation pipelines on Australian reference genomes.
The performance of Tiberius without RNAseq data made this tool the perfect candidate for rapid gene prediction on assemblies produced by the Genome Engine in the Australian BioCommon’s Australian Tree of Life (AToL) project. It has become an essential part of the Genome Engine that will enable rapid, automated assembly, annotation and publication of genomes.
While Tiberius was prioritised for inclusion because it’s an important part of the AToL project, individual researchers can also request the installation of new tools or datasets in Galaxy Australia. For researchers wanting to contribute to the international open source Galaxy community directly, there are supportive guidance videos for DIY tool wrapping. Proactive community members recently took up the challenge, and collaborated with BioCommons to make the first dedicated glycomics tool and workflow available on Galaxy.
Try out Tiberius in the Galaxy Australia Genome Lab
Register for the webinar Benchmarking the latest annotation pipelines on Australian reference genomes
