6c0944e7d8e0bb76773b6c3013b0a5fbd0e95ecf brianlee Thu Feb 6 10:45:07 2020 -0800 Adding message to utils about non-tested external tools and adding more links refs #24920 diff --git src/hg/htdocs/util.html src/hg/htdocs/util.html index 66d546c..d63feb9 100755 --- src/hg/htdocs/util.html +++ src/hg/htdocs/util.html @@ -1,64 +1,74 @@ <!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> </p> <p> 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: +file formats and the genome annotation databases that we provide. UCSC has not tested and does +not endorse any of these external tools. <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="https://github.com/Gaius-Augustus/MakeHub">MakeHub</a></strong> - Python tool to build assembly hubs files for new genomes </li> + <li><strong><a href="https://github.com/CRG-Barcelona/bwtool/wiki">bwtool</a></strong> - + A command-line utility for bigWig files + </li> + <li><strong><a href="https://bedtools.readthedocs.io/en/latest/">bedtools</a></strong> - + A swiss-army knife of tools for a wide-range of genomics analysis tasks + </li> + <li><strong><a href="https://bedops.readthedocs.io/en/latest/">BEDOPS</a></strong> - + A highly scalable and easily-parallelizable genome analysis toolkit + </li> </ul> </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->