Smaller software changes are not announced here. A summary of the three-weekly release changes can be here. For the full list of our daily code changes head to our GitHub page.
-We are proud to announce the release of four new tracks and a new track group on -hg38 dedicated to HPRC (Human Pangenome Reference Consortium) data.
+We are proud to announce the release of four new tracks and a new track +group on hg38 dedicated to the NIH's Human Pangenome Reference Consortium +(HPRC) data.
-The HPRC -aims to gather genomic data from diverse populations to better -represent the genomic landscape of diverse human populations. This is an important -endeavor in genomics as no single reference can accurately represent human diversity. -As described by the HPRC, using a single reference genome creates reference biases, -adversely affecting variant discovery, gene–disease association studies, and the -accuracy of genetic analyses. With this in mind, the HPRC was started to help -migrate common genomic analysis to use a pangenome so diverse populations are better represented.
+No single reference genome such as hg19 or hg38 can accurately represent +human genetic diversity. The HPRC's goal is to improve this by sequencing +thousands of human genomes at high quality and building new tools to +improve working with them. The first data release +from this project consists of 47 +phased, diploid assemblies, more than 99% accurate at the structural and +base pair levels. We obtained alignments of these new genomes to hg38 from +the HPRC analysis groups and have created new Genome Browser annotation +tracks that visualize the differences between the established hg38 +reference and the new 94 pan-genome assemblies. The new tracks are grouped +into short and structural variants, with the latter further split by type +(insertion, deletion, inversion, duplication, etc). We plan to update these +and add other tracks as soon as more HPRC data is released.
In this first HPRC data release, we are adding four new tracks to this new track group. @@ -175,31 +183,32 @@
The 90-way Multiple Alignment track contains multiple alignments of 90 human genomes generated by the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments. This method builds graphs containing all forms of genetic variation while allowing the use of current mapping and genotyping tools. The confirmation page sorts the Maternal and Paternal haplotypes by the same 14 subpopulations described above.
We are always looking for feedback, if you would like to see other HPRC data, or the data presented differently, please contact us at genome@soe.ucsc.edu. Likewise, if you find this data useful and see potential improvements, we would be interested in hearing from you.
We would like to thank the Human Pangenome Reference Consortium for taking on this genomics -challenge and providing these data. In particular, we would like to thank XXX, XXX, and XXX +challenge and providing these data. In particular, we would like to thank Benedict Paten, +Heng Li and Glenn Hickey for their help in putting these Browser tracks together. From our team, we would like to thank Max Haeussler, Brian Raney, Mark Diekhans, Hiram Clawson, Gerardo Perez, Jairo Navarro, and Lou Nassar for their work in developing, testing, and releasing these tracks.
We are excited to announce the release of the VISTA Enhancers tracks for human and mouse genome assemblies. These datasets were previously part of the VISTA Enhancers public hub and have now been incorporated natively into the Genome Browser to better serve the research community.
View the VISTA Enhancer track on the following assemblies: