795e0dfc543020d5a353f1c27291d31de17992ec mspeir Sat Mar 14 12:57:37 2026 -0700 minor tweak to genark entry, no refs diff --git docs/genomeBrowserGlossary.md docs/genomeBrowserGlossary.md index cccabcb5a44..cf0abdc8fe1 100644 --- docs/genomeBrowserGlossary.md +++ docs/genomeBrowserGlossary.md @@ -25,33 +25,34 @@ - [Conservation and Comparative Genomics](#conservation-and-comparative-genomics) - [Variants and Clinical Data](#variants-and-clinical-data) - [Regulatory and Functional Data](#regulatory-and-functional-data) - [Table Browser](#table-browser) - [Technical Terms](#technical-terms) ## Genome Assemblies and Nomenclature **Assembly**: A genome assembly is the complete genome sequence produced after chromosomes have been fragmented, sequenced, and computationally reassembled. Assemblies are updated when new sequence data fills gaps or improved algorithms produce better results. Find supported assemblies from the [gateway page](/cgi-bin/hgGateway) or request new ones from our [assembly search page](/assemblySearch.html). -**[GenArk](https://hgdownload.gi.ucsc.edu/hubs/)**: UCSC's Genome Archive +**[GenArk](https://hgdownload.gi.ucsc.edu/hubs/)**: UCSC's repository containing thousands of additional genome assemblies beyond the main featured -assemblies. +assemblies. Search for and request new ones from +our [assembly search page](/assemblySearch.html). **Chromosome Coordinates**: Genomic positions specified as chromosome name and base position (e.g., `chr7:155,799,529-155,812,871`). UCSC uses zero-based, half-open coordinates in its databases. See [this blog post](https://genome-blog.gi.ucsc.edu/blog/2016/12/12/the-ucsc-genome-browser-coordinate-counting-systems) for details. **Scaffold / Contig**: Intermediate sequence units used in genome assembly. A contig is a contiguous stretch of assembled sequence with no gaps, while a scaffold is an ordered set of contigs joined by estimated gap lengths. In assemblies that are not fully resolved into chromosomes, sequences may be named as scaffolds (e.g., `scaffold10671`) rather than chromosomes. In chromosome-based assemblies, unplaced scaffolds appear as sequences like `chrUn_gl000220` and unlocalized scaffolds (known chromosome, unknown position) appear as `chr1_gl000191_random`.