UCSC Genome Browser Utilities
The following tools and utilities created by the UCSC Genome Browser Group are available for
Batch Coordinate Conversion (liftOver) -
converts genome coordinates and genome annotation files between assemblies. The current version
supports both forward and reverse conversions, as well as conversions between selected
DNA Duster -
removes formatting characters and other non-sequence-related characters from an input sequence.
Offers several configuration options for the output format, including translated protein.
Duster - removes formatting characters and other non-sequence-related characters
from an input sequence. Offers several configuration options for the output format.
Phylogenetic Tree PNG Maker - creates a PNG image
from the phylogenetic tree specification given. Offers several configuration options for branch
lengths, normalized lengths, branch labels, legend etc.
Source Code Downloads - executable and source code downloads of the Genome Browser,
Blat and liftOver.
The following tools and utilities created by outside groups may be helpful when working with our
file formats and the genome annotation databases that we provide. References to these tools are
provided for the benefit of our users. We are unable to support the use of externally developed
tools; if you have questions or problems, please contact the developers of the tool directly.
- BEDOPS -
A highly scalable and easily-parallelizable genome analysis toolkit
- bedtools -
A swiss-army knife of tools for a wide-range of genomics analysis tasks
- bwtool -
A command-line utility for bigWig files
- CrossMap -
A program for genome coordinate conversion between different assemblies
- CruzDb -
Python package to load genome annotations from our servers
- libBigWig -
A C library to read bigWig files, without a dependency on our source code
- MakeHub -
Python tool to build assembly hub files for new genomes
- RTracklayer -
R package to import genome annotations from our databases
- trackhub -
Python package to manage files in our trackDb format
- twobitreader - Python package to open
2bit genome sequence files
- ucsc-genomes-download -
Python package to download genome sequences from our servers
- WiggleTools -
C++ Unix command-line tool to work with bigWig files: combine, merge, scale, aggregate and many other operations