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Aug. 04, 2021 Addition of GRCm38 patch 6 sequences to mm10

+ We are pleased to announce the addition of GRCm38 patch release 6 to the mm10 assembly. mm10 has + been updated with patches since its release in 2012. The GRC patch releases do not change any + previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes + that correspond to specific regions of the main chromosome sequences. For most users, the patches + are unlikely to make a difference and may complicate the analysis as they introduce more + duplication.

+ +

+ More information on how patch sequences are incorporated can be found on the + Patching up the Genome blog post. + The blog post contains details about the new + /latest, + /initial, and + /p6 + download directories on the downloads server. With the addition of new sequences to mm10, we can + expect to see BLAT return more matches to the genome.

+ +

+ The initial/ subdirectory contains files for the initial release of GRCm38, which has 66 + sequences, no original alternate sequences, and no fix sequences. It is the same as the + parent download directory. This is probably the best genome file for aligners and most analysis + tasks, a version called "analysisSet" for the human genome. +
+ The p6/ subdirectory contains files for GRCm38.p6 (patch release 6). It has 239 sequences + including alternate and fix sequences. Note that these patches include + "strain-specific" sequences. You may want to check with the authors of your aligner if + the software can recognize these sequences. +
+ The latest/ symbolic link points to the subdirectory for the most recent patch version. +

+ +

+ We would like to thank the Genome + Research Consortium for creating the patches for mm10. We would also like to thank Galt Barber + and Jairo Navarro at UCSC for implementing and testing the latest patch to the mm10 genome.

+ + +

Aug. 02, 2021 New Genome Browser: X. tropicalis, xenTro10 (Xenopus tropicalis)

+ A genome browser is now available for the Xenopus tropicalis assembly released in Nov. 2019 by the + University of California, Berkeley (UCB_Xtro_10.0). +

About the assembly:

UCSC Genome Browser assembly ID: xenTro10
Sequencing/Assembly provider ID: + University of California, Berkeley
Assembly date: Nov. 2019
Accession ID: GCF_000004195.4
NCBI Genome ID: 80 (Xenopus tropicalis)
NCBI Assembly ID: 5323661
NCBI BioProject ID: 577946
NCBI BioSample ID: SAMN16261960
Scaffold count: 167
Total size: 1,451,301,209
Acknowledgments

Data and Downloads:

+ We would like to thank the University of California, Berkeley for creating this new X. tropicalis assembly. + We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for the development and release of + the xenTro10 genome browser. +

July 20, 2021 Updated GENCODE tracks released for hg38, hg19, and mm39

We have updated our GENCODE gene datasets to the latest releases; v38 for human (hg38 & hg19) and v27 for the mouse genome assembly (mm39). These new annotation data were released by GENCODE in May 2021 and correspond to the Ensembl Genes 104 dataset.

These tracks can be found in our All GENCODE super-track folder, with subset tracks and abundant filter options. This super-track contains many previous versions of the GENCODE genes for easy comparison. From the - + GENCODE stats page, this updated dataset has approximately 60.6k genes and 237k transcripts on the human hg38 assembly.

For more information or to visualize the data, you can visit the following track description pages: