Manual annotation learning and training resources
We’ve put together resources to help you learn more about manual annotation, in particular via the Apollo software – whether you’re new to manual annotation, are looking to train undergraduates in manual annotation, or just need more information.
What is manual annotation, and how does Apollo help me do it?
There are a number of definitions of manual annotation. Within the Apollo context, it means the manual improvement of a gene prediction – both the structural (e.g. the protein and transcript sequence) and functional (e.g. the name and other metadata) components. Apollo is a software package that greatly simplifies the manual annotation process via a user-friendly web interface. The i5k Workspace@NAL provides the Apollo software for all of the genome projects that we host.
New to manual annotation and Apollo, or need a refresher? We recommend the following tutorials:
- We have our own, of course (contact firstname.lastname@example.org if you’d like a recording): https://i5k.nal.usda.gov/sites/default/files/presentations/Apollo_training_8-2019.pdf; https://i5k.nal.usda.gov/sites/default/files/i5k_training/Web_Apollo_Workshop_Example.pdf
- Monica Munoz-Torres, an Apollo project alumna, provides an excellent overview and dives into the details: https://www.slideshare.net/MonicaMunozTorres/presentations
- The Nescent-funded Genome Train has a number of resources to get you started: http://genomecuration.github.io/genometrain/d-feature-curation-crossing/index.html
- Alexie Papanicolaou from the Hawkesbury Institute for the Environment developed a useful tutorial: https://stressedfruitfly.com/tutorial-curation-snmp1/
- Rob Waterhouse’s Apollo training session with BIPAA, the BioInformatics Platform for Agroecosystem Arthropods: https://www.youtube.com/watch?v=BMeSwdKiO_E
Working with undergraduates?
- Surya Saha et al. propose “A quick guide for student-driven community genome annotation”: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006682
- The Genomics Education Partnership has a number of great materials for undergraduate training: http://gep.wustl.edu/curriculum/introducing_genes; http://gep.wustl.edu/curriculum/workshop_materials
- Genome Solver is focused on microbial genomics and provides some useful background: https://qubeshub.org/community/groups/genomesolver/resource
Need a deeper dive?
- The official Apollo user guide: https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html
- The i5k Workspace’s Annotation guidelines: https://i5k.nal.usda.gov/content/rules-web-apollo-annotation-i5k-pilot-project
- The i5k Workspace’s gene and protein nomenclature guidelines: https://i5k.nal.usda.gov/i5k-workspace-gene-and-protein-naming-guidelines
- Mapped RNA-Seq reads are incredibly useful for manual annotation. Here’s how to map your RNA-Seq reads to an i5k Workspace genome: https://i5k.nal.usda.gov/mapping-rna-seq-reads-manual-curation-faq
The i5k Workspace@NAL offers manual annotation resources via Apollo. Feel free to get in touch with us if you need Apollo set up for your genome! That said, our resources don’t always fit everyone’s needs. If you need to branch out, here are some resources that may be useful to you:
- G-OnRamp: A Galaxy-based alternative to Apollo. http://gonramp.wustl.edu/?page_id=1031
- GenSas: A portal to predict genes on a genome assembly and curate them with Apollo. https://www.gensas.org/
Just need your own genome browser?
- National Center for Genome Analysis and Synthesis lets you spin up a pop-up browser: https://ncgas.org/WelcomeBasket_PopUpBrowser.php
- CoGe lets you set up a private browser quickly: https://genomevolution.org/wiki/index.php/Tutorials#How_to_load_a_private_genome_with_annotations_and_experimental_data.2C_and_view_in_JBrowse_in_under_three_minutes