BigWig and BigBed: enabling browsing of large distributed datasets.

Bioinformatics
W J KentD Karolchik

Abstract

BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu.

References

Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Nov 13, 2009·Nucleic Acids Research·Brooke RheadW James Kent

❮ Previous
Next ❯

Citations

Dec 1, 2011·Nature Methods·Xin ZhouTing Wang
Sep 19, 2012·Nature Reviews. Genetics·Christoph Bock
Jan 27, 2011·Briefings in Functional Genomics·Martin Hirst, Marco A Marra
Apr 21, 2012·Briefings in Bioinformatics·Helga ThorvaldsdóttirJill P Mesirov
Aug 22, 2012·Briefings in Bioinformatics·Robert M KuhnW James Kent
Jan 22, 2011·Bioinformatics·Thomas A DownTim J P Hubbard
Mar 16, 2012·Bioinformatics·Kris Popendorf, Yasubumi Sakakibara
Dec 12, 2012·Bioinformatics·Theodore R Pak, Frederick P Roth
Mar 12, 2013·Bioinformatics·Jingjing JinNam-Hai Chua
Mar 22, 2012·Database : the Journal of Biological Databases and Curation·Esther T Chan, J Michael Cherry
Nov 3, 2010·Nucleic Acids Research·Brian J RaneyW James Kent
Oct 21, 2010·Nucleic Acids Research·Pauline A FujitaW James Kent
Nov 15, 2011·Nucleic Acids Research·Kate R RosenbloomW James Kent
Nov 17, 2011·Nucleic Acids Research·Timothy R DreszerW James Kent
Nov 15, 2011·Nucleic Acids Research·Patricia P ChanTodd M Lowe
Nov 30, 2012·Nucleic Acids Research·René DreosPhilipp Bucher
Jul 9, 2011·BMC Bioinformatics·P Alexander Rolfe, David K Gifford
Jan 3, 2012·BMC Bioinformatics·Sveinung GundersenGeir Kjetil Sandve
Sep 22, 2012·BMC Bioinformatics·Hiroyuki MishimaKoh-ichiro Yoshiura
Dec 7, 2013·BMC Bioinformatics·Jerome KelleherDaniel L Halligan
Aug 24, 2011·Genome Biology·Tao LiuX Shirley Liu
Sep 7, 2012·Genome Biology·Xianjun DongZhiping Weng
Sep 5, 2013·Genome Biology·Eduardo LeeSuzanna E Lewis
Oct 1, 2011·Genome Medicine·Stephanie Om Dyke, Tim Jp Hubbard
Mar 13, 2014·Nature Chemical Biology·Lucas T GrayNancy Maizels
Feb 4, 2014·Bioinformatics·Andy Pohl, Miguel Beato
May 29, 2014·Bioinformatics·Do Huy Hoang, Wing-Kin Sung
Jul 1, 2014·BMC Genomics·Ting-Wen ChenPetrus Tang
May 7, 2014·Nucleic Acids Research·Liran JuanYadong Wang
Nov 27, 2014·Database : the Journal of Biological Databases and Curation·Peng ZhangDa-Wei Huang
Nov 19, 2013·PLoS Computational Biology·Timothy BaileyJie Zhang
Nov 22, 2015·Nucleic Acids Research·Matthew L SpeirW James Kent
Nov 4, 2015·Nucleic Acids Research·Cricket A SloanJ Michael Cherry
Dec 22, 2015·Nucleic Acids Research·Andrew YatesPaul Flicek

❮ Previous
Next ❯

Software Mentioned

BigBed
bigWigToBedGraph
Solexa
bigWigSummary
bigWigToWig
gzip
bedGraph
autoSql
Perl
bigBedToBed

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.