[IGBF-3823] Add genomes requested at SDB2024 to IGB - JIRA UNCC

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Type: Epic
Status: To-Do (View Workflow)
Priority: Major
Resolution: Unresolved
Affects Version/s: None
Fix Version/s: None
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Epic Name:
Add genomes requested during SDB

Description

Situation: We talked to several individuals at SDB2024 that do research with species we don't currently support in IGB (see below). These genomes don't appear to be available on either ensembl or UCSC, only NCBI.

Task: Make separate tickets to add or update the following genomes in IGB:

Hymenolepis diminuta
Mnemiopsis leidyi (mnemiopsis.leidyi.v3) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_963919725.1/
Update the Oryzias latipes genome to the 2017 version (ASM223467v1) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002234675.1/
Capitella teleta (Capca1) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000328365.1/
Hydra vulgaris (HydraT2T_AEP) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_038396675.1/
Triops longicaudatus (TLON_2021) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_022885665.1/
Vanessa cardui

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Nowlan Freese added a comment - 05/Sep/24 10:52 AM - edited

Some notes from Nowlan on how to get started with adding new genomes to IGB

See ~~IGBF-3330~~ for some additional notes on adding a recent genome to IGB.
This is the primary document with instructions for adding a genome to IGB: How we add new genomes to IGB Quickload using UCSC Genome Informatics as a data source
After preparing the files you will need to push them to our subversion repository. The main document with example commands is: Setting up the Quickload subversion repository on EC2 with EBS
You can see the subversion repository here: https://svn.bioviz.org/viewvc/genomes/quickload/
GenomeSource repository: https://bitbucket.org/lorainelab/genomesource/src/master/
Gene_info files can be found here: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

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Nowlan Freese added a comment - 05/Sep/24 10:52 AM - edited Some notes from Nowlan on how to get started with adding new genomes to IGB See IGBF-3330 for some additional notes on adding a recent genome to IGB. This is the primary document with instructions for adding a genome to IGB: How we add new genomes to IGB Quickload using UCSC Genome Informatics as a data source After preparing the files you will need to push them to our subversion repository. The main document with example commands is: Setting up the Quickload subversion repository on EC2 with EBS You can see the subversion repository here: https://svn.bioviz.org/viewvc/genomes/quickload/ GenomeSource repository: https://bitbucket.org/lorainelab/genomesource/src/master/ Gene_info files can be found here: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

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Assignee:

Paige Kulzer

Reporter:

Paige Kulzer

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Dates

Created:

23/Jul/24 2:50 PM

Updated:

13/Dec/24 3:20 PM