Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

• Published in: Bioinformatics Vol. 30; no. 7; pp. 1003 - 1005
• Main Authors: Raney, Brian J., Dreszer, Timothy R., Barber, Galt P., Clawson, Hiram, Fujita, Pauline A., Wang, Ting, Nguyen, Ngan, Paten, Benedict, Zweig, Ann S., Karolchik, Donna, Kent, W. James
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.04.2014
• Subjects: Annotations; Applications Notes; Bioinformatics; Collection; Databases, Genetic; Genome; Genomes; Genomics - methods; Hubs; Internet; Software; Summaries; Visualization
• ISSN: 1367-4803; 1367-4811; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btt637

Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu. Contact:  donnak@soe.ucsc.edu