7ef475c3faf058d5248baa20520901a9b3f84da7 brianlee Wed Feb 5 08:48:17 2020 -0800 Adding MakeHub to Max's new addition of utilities refs #24666 diff --git src/hg/htdocs/util.html src/hg/htdocs/util.html index eb1a0cf..fedd287 100755 --- src/hg/htdocs/util.html +++ src/hg/htdocs/util.html @@ -1,61 +1,63 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Utilities" --> <!--#set var="ROOT" value="." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>UCSC Genome Browser Utilities</h1> <p> The following tools and utilities created by the UCSC Genome Browser Group are available for public use:</p> <ul class="gbsNoBullet"> <li> <strong><a href="cgi-bin/hgLiftOver">Batch Coordinate Conversion (liftOver)</a></strong> - converts genome coordinates and genome annotation files between assemblies. The current version supports both forward and reverse conversions, as well as conversions between selected species.</li> <li> <strong><a href="http://users.soe.ucsc.edu/~kent/dnaDust/dnadust.html">DNA Duster</a></strong> - removes formatting characters and other non-sequence-related characters from an input sequence. Offers several configuration options for the output format, including translated protein.</li> <li> <strong><a href="http://users.soe.ucsc.edu/~kent/protDust/protDust.html">Protein Duster</a></strong> - removes formatting characters and other non-sequence-related characters from an input sequence. Offers several configuration options for the output format.</li> <li> <strong><a href="cgi-bin/phyloPng">Phylogenetic Tree PNG Maker</a></strong> - creates a PNG image from the phylogenetic tree specification given. Offers several configuration options for branch lengths, normalized lengths, branch labels, legend etc.</li> <li> <strong><a href="http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads">Executable and Source Code Downloads</a></strong> - executable and source code downloads of the Genome Browser, Blat and liftOver.</li> </ul> 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: public use:</p> <ul class="gbsNoBullet"> <li> <strong><a href="https://bioconductor.org/packages/release/bioc/html/rtracklayer.html">RTracklayer</a></strong> - R package to import genome annotations from our databases</li> <li><strong><a href="https://pypi.org/project/twobitreader/">twobitreader</a></strong> - Python package to open 2bit genome sequence files</li> <li><strong><a href="https://pypi.org/project/cruzdb/">CruzDb</a></strong> - Python package to load genome annotations from our servers</li> <li><strong><a href="https://pypi.org/project/ucsc-genomes-downloader/">ucsc-genomes-download</a></strong> - Python package to download genome sequences from our servers </li> <li><strong><a href="https://daler.github.io/trackhub/">trackhub</a></strong> - Python package to manage files in our trackDb format </li> <li><strong><a href="https://github.com/Ensembl/WiggleTools">WiggleTools</a></strong> - C++ Unix command-line tool to work with bigWig files: combine, merge, scale, aggregate and many other operations. </li> <li><strong><a href="https://github.com/dpryan79/libBigWig">libBigWig</a></strong> - A C library to read bigWig files, without a dependency on our source code </li> - <li><strong><a href=""></a></strong> - + <li><strong><a href="https://github.com/Gaius-Augustus/MakeHub">MakeHub</a></strong> - + Python tool to build assembly hubs files for new genomes </li> +</ul> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->