Presentation of cassavabase, its goal and current main features for cassava breeding and genomics

1. -> Cassavabase and other RTB databases
-> What is new?
-> Account request and login
CASSAVABASE

2. • Introduction
-> Cassavabase and sister RTB databases
-> What s new?
-> Account request and login
• “Search” menu
-> Search accessions and trials plots (+people & marker data)
-Use single or multiple fields search (wizard search)
-> Login Create and use list to manage accessions, trials and traits
• "Manage” menu
-> Manage breeding programs & locations
-create new breeding programs & locations
-> Manage accessions
-search, accession detail page, pedigree editing, find related trial and population
-> Manage crosses
-create and edit populations, define parents and siblings
-> Manage trials
- 1a- export from Cassavabase an existing trial file
- 1b- Import to Cassavabase an existing trial file
- 2- Create in Cassavabase a new trial using accession list
- 3- Access and edit existing trials & informations:
- field map
- field design
- available accessions and plots
- available phenotypic traits
- 4- Upload/Download features for Phenotypic traits assayed in the trial using Field Book
-> Manage genotyping trials
-create genotyping experiment to perform and create submission spreadsheet to Cornell sequencing facility
-> Manage Fieldbook app
-create field layout files for field book, uplad data from fieldbook to cassavabase
-> Manage phenotypes
-upload phenotypic data in trial experiments
-> Manage barcodes
-create barcodes for field phenotyping
-> Manage download
-download phenotypic and genotypic bulk data (multiple trials, traits &accessions)
• ”Analyze” menu
-> SolGS genomic selection tools,
-> Vizualise GBS sequence data with Jbrowse, perform BLAST, use the Cassava VIGS tool
• Contact
-> Contact us! Cassavabase tutorials and websites
Tutorial overview

3. https://github.com/solgenomics
https://cassavabase.org
https://yambase.org
https://sweetpotatobase.org
https://musabase.org

4. The Central data store for NEXTGEN CASSAVA :
Genomic selection in African cassava breeding programs
http://nextgencassava.org/
• Cassavabase is open to ALL cassava breeders!

5. Why Databases?
• Data Archiving
• Data Accessibility
• Data Integration
• Data sharing
• Better data analysis

6. What do you need to use
Cassavabase?

7. https://cassavabase.org/

8. https://yambase.org/

9. https://sweetpotatobase.org/

10. https://musabase.org/

11. New responsive design

12. Caroussel

13. New search bar
Navigation bar always visible on top Expandable search box

14. Data content
+360 registered users
• ~80,000
accessions
• ~300,000
trial plots
• ~8,000,000
phenotypic observations
• ~2 billion genotypic
datapoints

15. CASSAVABASE users

16. Accounts
Account Type Privileges
none Browse, use tools
“user" User database, forum
“submitter"
create trials, add phenotype information
etc.

17. Create Account

18. Sign up link
Create Account

19. Email Notification!