Manual annotation learning and training resources

What is manual annotation, and how does Apollo help me do it? 

How do I get an account to annotate in Apollo? 

Tutorials on manual annotation and Apollo

• A general overview of manual annotation, with a worked example (contact i5k@ars.usda.gov if you’d like a recording): https://i5k.nal.usda.gov/sites/default/files/presentations/Apollo_training_8-2019.pdf
• An overview of the various functions of Apollo (contact i5k@ars.usda.gov if you’d like a recording): https://i5k.nal.usda.gov/sites/default/files/presentations/Apollo_webinar_8-18-2021.pdf  
• The i5k Workspace’s gene and protein nomenclature guidelines: https://i5k.nal.usda.gov/i5k-workspace-gene-and-protein-naming-guidelines
• 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/themes/stressedfruitfly/assets/videos/snmp1_webapollo1_960.mp4
• Rob Waterhouse’s Apollo training session with BIPAA, the BioInformatics Platform for Agroecosystem Arthropods: https://www.youtube.com/watch?v=BMeSwdKiO_E 

Manual annotation with undergraduate students 

• Manual annotation with Apollo can be an excellent way to engage undergraduates. We encourage and support undergraduate annotation at the i5k Workspace@NAL. Get in touch with us if you are planning undergraduate annotation with i5k Workspace@NAL resources.
• For smaller groups of undergraduates with in-depth capstone projects, we recommend the guidelines proposed in “A quick guide for student-driven community genome annotation” by Prashant Hosmani et al.: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006682
• For larger undergraduate courses, we recommend the Genomics Education Partnership. This organization provides a number of excellent 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/

Additional documentation

• 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
• Functional annotations:
  • Webinar slides on how to incorporate functional annotations into your manual annotation workflow: https://i5k.nal.usda.gov/sites/default/files/presentations/func-annot-webinar-12-2022.pdf 
  • The AgBase functional annotation pipeline that we use to generate functional annotations: https://agbase-docs.readthedocs.io/en/latest/agbase/workflow.html 
• The pipeline we use to map RNA-Seq reads to genomes and load them to JBrowse: https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline

Other software

• G-OnRamp: A Galaxy-based alternative to Apollo. https://g-onramp.org/index.html
• 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?
  • 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

Do you have suggestions for improving this list of resources? Contact us – we love feedback.