Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Spring 1, Spring 2, Spring 3, Spring 4
Description
Task: Add the Aedes albopictus (Asian tiger mosquito) genome and annotation to IGB. Current Aedes albopictus genome version provided by NCBI RefSeq: GCF_035046485.1.
Aedes albopictus (AalbF5)(Jan 2024) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_035046485.1/
Documentation to follow: https://docs.google.com/document/d/1v9caFNNQK-Az_7ztAV6TTMUbm9LUajvbnD-QBJpcSwY/edit?usp=sharing
Attachments
Activity
Tested on Mac with main branch installer.
- Aedes albopictus appears in the Species dropdown with the correct synonyms.
- Gene models and the sequence loads (2bit located at UCSC).
- Quickload page loads.
- ISSUE - The ncbi link is not working. Because it is not a full URL the webpage assumes it is a relative path. Update to be a full path: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_035046485.1/
- Note that this issue is also present for
- Capitella teleta
- Hydra vulgaris
- Oryzias latipes
- Vanessa cardui
I've pushed changes to the HEADER.md files for all of the above listed genomes. Dr. Loraine created a template HEADER.md file as part of IGBF-4038, so that is the new format I followed here. The SVN repository is now at revision 227. Ready for review!
Tested Header.md for the following genomes. All links are working correctly.
- Aedes albopictus
- Capitella teleta
- Hydra vulgaris
- Oryzias latipes
- Vanessa cardui
Ready to be deployed.
I have deployed the new repository to our hosting at RENCI (the default quickload site) and to our hosting at charlotte. Ready for final testing.
To test, I visited each page for the above listed genome versions, hosted on our QL site.
For example, the V. cardui quickload page is: http://igbquickload-main.bioviz.org/quickload/V_cardui_Feb_2021/
All the links worked.
Moving to Done.
I've placed a zipped version of the new quickload folder in Google Drive for the reviewer to take a look at:
Path: research-big-lorainelab > IGB Project Documentation and Plans > IGB Genomes > A_albopictus.zip
Link: https://drive.google.com/drive/folders/1bFRx4PqldxNf400n7Vr9SD_dNeNmtpvk?usp=drive_link
Question for the reviewer: If there's no manuscript published which details more about the genome assembly and its annotations, is there any other info I should provide in HEADER.md for IGB Quickload users to reference?