Apollo and genome assembly updates

We have 2 important topics to announce. We encourage you to read through this entire email to minimize disruption for your work at the i5k Workspace.

Transition to new genome assemblies

Most of the i5k pilot species now have updated genome assemblies (https://www.ncbi.nlm.nih.gov/assembly/?term=i5k).The i5k Workspace wants to migrate its resources to the next assembly version, but also needs your feedback on when to do the migration. This migration may significantly disrupt ongoing annotation efforts. Therefore, we are surveying the community for your annotation plans, in order to minimize the disruption for your work. The survey below gauges annotation activity for a subset of the i5k pilot organisms. Please complete the survey by October 23^rd, 2018.

https://docs.google.com/forms/d/1bmBMy_70WWd1OiGP8ZD8FIGfARjXgyMb0xHq2HAXwHw/

Transition to the Apollo2 software

We are transitioning many of our genome browsers from the Apollo1 to the Apollo2 software.

Apollo2 has many more functions and features than Apollo1. You can find training and documentation on Apollo2 here:

• The official Apollo user guide: http://genomearchitect.github.io/users-guide/
• Tutorials on using Apollo2:
  • https://www.slideshare.net/MonicaMunozTorres/apollo-workshop-ags2017-introduction
  • https://www.slideshare.net/MonicaMunozTorres/apollo-workshop-ags2017-editing-functionality
  • https://i5k.nal.usda.gov/sites/default/files/presentations/Apollo_training_AGS_2018.pdf

We have updated the software version and browser URLs for Apollo for the following 10 organisms. You can also find all up-to-date browser URLs here: https://i5k.nal.usda.gov/available-genome-browsers

• Anoplophora glabripennis: https://apollo.nal.usda.gov/apollo/Anoplophora%20glabripennis/jbrowse/
• Athalia rosae: https://apollo.nal.usda.gov/apollo/Athalia%20rosae/jbrowse/
• Blattella germanica: https://apollo.nal.usda.gov/apollo/Blattella%20germanica/jbrowse/
• Cephus cinctus: https://apollo.nal.usda.gov/apollo/Cephus%20cinctus/jbrowse/
• Cimex lectularius: https://apollo.nal.usda.gov/apollo/Cimex%20lectularius/jbrowse/
• Frankliniella occidentalis: https://apollo.nal.usda.gov/apollo/Frankliniella%20occidentalis/jbrowse/
• Gerris buenoi: https://apollo.nal.usda.gov/apollo/Gerris%20buenoi/jbrowse/
• Hyalella azteca: https://apollo.nal.usda.gov/apollo/Hyalella%20azteca/jbrowse/
• Oncopeltus fasciatus: https://apollo.nal.usda.gov/apollo/Oncopeltus%20fasciatus/jbrowse/
• Orussus abietinus: https://apollo.nal.usda.gov/apollo/Orussus%20abietinus/jbrowse/

We will transition the remaining Apollo1 browsers in due course. Genomes with active annotation efforts will be transitioned once the annotation effort is complete.