Create Telomere to Telomere human genome Quickload

Ann Loraine added a comment - 17/Sep/24 11:23 AM - edited As per discussion with Nowlan Freese after scrum, we would like to do these two things: Use species name "Homo sapiens T2T" for "human telomere to telomere reference" This is to allow this assembly to exist alongside the traditional hg38, hg19, etc assemblies. We want to do this because so many people are 100% using hg38 and hg19, not this new assembly just yet. The version should be something like: H_sapiens_T2T_MMM_YYYY Note that we need to be super duper careful about making sure that our version dates map correctly onto UCSC patch releases, or whatever they are doing to keep track of how the sequence itself (and all the constituent contigs) changes over time. Instead of version-controlling the 2bit file in our subversion repository, let's "reference=TRUE" tag in annots.xml and have the file name be the URL of the 2bit file hosted on the UCSC genome web site. This will enable IGB to locally cache the genome file instead of always having to use the JSON REST API to retrieve sequence data all the time. Also, retrieving data from a 2bit file may be faster than getting sequence data from the JSON REST API. Testing : Make sure that IGB can also retrieve sequence data from the JSON REST API in case the URL of the 2bit file changes or the UCSC Web site messes up somehow. To do this, a tester can edit the "file" tag to point to a bogus location. If everything works the way it is supposed to work, then the user won't even notice that the 2bit file is missing and will simply default to getting data from the UCSC JSON API. However, note that the "load priority" numbers are related to which data source IGB retrieves sequence data from.