Releases: BaderLab/GenAnT
Tutorial: annotation of animal genomes
Version of GenAnT at the time of publication.
Reference: Clarke, Z.A., Sokolowski, D.J., Byles-Ho, C.K. et al. Tutorial: annotation of animal genomes. Nat Protoc (2026). https://doi.org/10.1038/s41596-025-01301-1
Abstract: As DNA sequencing technologies improve, it is becoming easier to sequence and assemble new genomes from non-model organisms. However, before a newly assembled genome sequence can be used as a reference, it must be annotated with genes and other features. This can be conducted by individual laboratories using publicly available software. Modern genome annotations integrate gene predictions from the assembled DNA sequence with gene homology information from other high-quality reference genomes and take into account functional evidence (e.g., protein sequences and RNA sequencing information). Many genome annotation pipelines exist but have varying accuracies, resource requirements and ease of use. This genome annotation Tutorial describes a streamlined genome annotation pipeline that can create high-quality genome annotations for animals in the laboratory. Our workflow integrates existing state-of-the-art genome annotation tools capable of annotating protein-coding and non-coding RNA genes. This Tutorial also guides the user on assigning gene symbols and annotating repeat regions. Finally, we describe additional tools to assess annotation quality and combine and format the results.
Pipeline:Paired with the educational resources, we provide a Snakemake pipeline to perform end-to-end annotations. On our end, a typical genome annotation takes 4-5h of human time and 4-5 days of runtime.
GenAnT release before tutorial is officially published
We provide a step-by-step tutorial to generate high-quality end-to-end genome annotations in the GENome ANnotation Tutorial (GenAnT). We also provide a series of shell scripts to run each step individually. Lastly, we provide a Snakemake pipeline to generate end-to-end annotations in one line of code + a config file. We are in the mature stages of the peer-review process. This current version has been tested by us and others and functions well. Upon publication we will generate any required updates and fixes before releasing the 1.0.0 version of GenAnT.