Sequence and Annotation Downloads

This page contains links to sequence and annotation data downloads for the genome assemblies featured in the UCSC Genome Browser. Table downloads are also available via the Genome Browser FTP server. For quick access to the most recent assembly of each genome, see the current genomes directory. This directory may be useful to individuals with automated scripts that must always reference the most recent assembly. To query and download data in JSON format, use our JSON API.

To view the current descriptions and formats of the tables in the annotation database, use the "describe table schema" button in the Table Browser.

All tables in the Genome Browser are freely usable for any purpose except as indicated in the README.txt files in the download directories. To view restrictions specific to a particular data set, click on the corresponding download link and review the README text. These data were contributed by many researchers, as listed on the Genome Browser credits page. Please acknowledge the contributor(s) of the data you use.

Human

Mouse

Mammals

Other vertebrates

Deuterostomes

Insects

Nematodes

Other genomes

Other downloads

Source and utilities downloads

The source for the Genome Browser, Blat, liftOver and other utilities is free for non-profit academic research and for personal use. For information on commercial licensing, see the Genome Browser and Blat licensing requirements. The source and executables for several of these products can be downloaded or purchased from our online store.

Mirroring the Genome Browser

Precompiled executable binaries are available for installing a local mirrored copy of the Genome Browser website on your web server, eliminating the need to compile the entire source tree.

If you encounter difficulties with slow download speeds, try using UDT Enabled Rsync (UDR), which improves the throughput of large data transfers over long distances. The 32-bit and 64-bit versions can be downloaded here.

Utilities

The utilities directory offers downloads of pre-compiled standalone binaries for:

LiftOver (which may also be accessed via the web version). The over.chain liftOver conversion files are located in the individual assembly download sections.

Blat Source code download (look for the blatSrc* zip file with the most recent date) Blat documentation The utilities directory contains pre-compiled standalone blat, gfServer, and gfClient binaries nested within a blat subdirectory for each system

Other command-line utilities

Note about 'permission denied' error:

In order for your computer to run a freshly downloaded utility, you will need to update the file system permissions to allow your operating system to run the program.

To make utilities usable, turn on its 'executable' bit:

$ chmod +x ./filePath/utility_name

$ ./filePath/utility_name

$ chmod +x /home/user/liftover/liftOver

Example:See also: http://en.wikipedia.org/wiki/Chmod

Please review the userApps README for information on fetching specific directories from the kent source tree or downloading userApps.src.tgz to install all kent utilities.

Note that commercial download and installation of the Blat and In-Silico PCR software requires a licence, which may be obtained from Kent Informatics.

Human genome

Dec. 2013 (GRCh38/hg38)

Feb. 2009 (GRCh37/hg19)

Mar. 2006 (NCBI36/hg18)