Literature DB >> 22411711

Visualizing next-generation sequencing data with JBrowse.

Oscar Westesson1, Mitchell Skinner, Ian Holmes.   

Abstract

JBrowse is a web-based genome browser, allowing many sources of data to be visualized, interpreted and navigated in a coherent visual framework. JBrowse uses efficient data structures, pre-generation of image tiles and client-side rendering to provide a fast, interactive browsing experience. Many of JBrowse's design features make it well suited for visualizing high-volume data, such as aligned next-generation sequencing reads.

Mesh：

Year:  2012        PMID： 22411711      PMCID： PMC3603211          DOI： 10.1093/bib/bbr078

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN： 1467-5463            Impact factor:   11.622


  12 in total

1.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

2.  The generic genome browser: a building block for a model organism system database.

Authors:  Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

3.  The Bioperl toolkit: Perl modules for the life sciences.

Authors:  Jason E Stajich; David Block; Kris Boulez; Steven E Brenner; Stephen A Chervitz; Chris Dagdigian; Georg Fuellen; James G R Gilbert; Ian Korf; Hilmar Lapp; Heikki Lehväslaiho; Chad Matsalla; Chris J Mungall; Brian I Osborne; Matthew R Pocock; Peter Schattner; Martin Senger; Lincoln D Stein; Elia Stupka; Mark D Wilkinson; Ewan Birney
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

4.  The Ensembl Web site: mechanics of a genome browser.

Authors:  James Stalker; Brian Gibbins; Patrick Meidl; James Smith; William Spooner; Hans-Rudolf Hotz; Antony V Cox
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

5.  Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.

Authors:  Alexander V Alekseyenko; Christopher J Lee
Journal:  Bioinformatics       Date:  2007-01-18       Impact factor: 6.937

6.  JBrowse: a next-generation genome browser.

Authors:  Mitchell E Skinner; Andrew V Uzilov; Lincoln D Stein; Christopher J Mungall; Ian H Holmes
Journal:  Genome Res       Date:  2009-07-01       Impact factor: 9.043

7.  Using Chado to store genome annotation data.

Authors:  Pinglei Zhou; David Emmert; Peili Zhang
Journal:  Curr Protoc Bioinformatics       Date:  2006-01

8.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

9.  Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Authors:  Ryan Lister; Ronan C O'Malley; Julian Tonti-Filippini; Brian D Gregory; Charles C Berry; A Harvey Millar; Joseph R Ecker
Journal:  Cell       Date:  2008-05-02       Impact factor: 41.582

10.  Dalliance: interactive genome viewing on the web.

Authors:  Thomas A Down; Matias Piipari; Tim J P Hubbard
Journal:  Bioinformatics       Date:  2011-01-19       Impact factor: 6.937
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  42 in total

Review 1.  Navigating and mining modENCODE data.

Authors:  Nathan Boley; Kenneth H Wan; Peter J Bickel; Susan E Celniker
Journal:  Methods       Date:  2014-03-15       Impact factor: 3.608

2.  Absence of the KhpA and KhpB (JAG/EloR) RNA-binding proteins suppresses the requirement for PBP2b by overproduction of FtsA in Streptococcus pneumoniae D39.

Authors:  Jiaqi J Zheng; Amilcar J Perez; Ho-Ching Tiffany Tsui; Orietta Massidda; Malcolm E Winkler
Journal:  Mol Microbiol       Date:  2017-11-02       Impact factor: 3.501

3.  Xenbase: Core features, data acquisition, and data processing.

Authors:  Christina James-Zorn; Virgillio G Ponferrada; Kevin A Burns; Joshua D Fortriede; Vaneet S Lotay; Yu Liu; J Brad Karpinka; Kamran Karimi; Aaron M Zorn; Peter D Vize
Journal:  Genesis       Date:  2015-07-16       Impact factor: 2.487

Review 4.  Xenopus genomic data and browser resources.

Authors:  Peter D Vize; Aaron M Zorn
Journal:  Dev Biol       Date:  2016-03-31       Impact factor: 3.582

5.  Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei.

Authors:  Sinclair Cooper; Elizabeth S Wadsworth; Torsten Ochsenreiter; Alasdair Ivens; Nicholas J Savill; Achim Schnaufer
Journal:  Nucleic Acids Res       Date:  2019-12-02       Impact factor: 16.971

6.  GeneDig: a web application for accessing genomic and bioinformatics knowledge.

Authors:  Radu M Suciu; Emir Aydin; Brian E Chen
Journal:  BMC Bioinformatics       Date:  2015-02-28       Impact factor: 3.169

7.  Polygenic inheritance of cryptorchidism susceptibility in the LE/orl rat.

Authors:  Julia Spencer Barthold; Joan Pugarelli; Madolyn L MacDonald; Jia Ren; Modupeore O Adetunji; Shawn W Polson; Abigail Mateson; Yanping Wang; Katia Sol-Church; Suzanne M McCahan; Robert E Akins; Marcella Devoto; Alan K Robbins
Journal:  Mol Hum Reprod       Date:  2015-10-26       Impact factor: 4.025

8.  Detection of Dual IDH1 and IDH2 Mutations by Targeted Next-Generation Sequencing in Acute Myeloid Leukemia and Myelodysplastic Syndromes.

Authors:  Mia Y Platt; Amir T Fathi; Darrell R Borger; Andrew M Brunner; Robert P Hasserjian; Leonora Balaj; Amy Lum; Stephen Yip; Dora Dias-Santagata; Zongli Zheng; Long P Le; Timothy A Graubert; A John Iafrate; Valentina Nardi
Journal:  J Mol Diagn       Date:  2015-08-30       Impact factor: 5.341

9.  CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea.

Authors:  Dadakhalandar Doddamani; Aamir W Khan; Mohan A V S K Katta; Gaurav Agarwal; Mahendar Thudi; Pradeep Ruperao; David Edwards; Rajeev K Varshney
Journal:  Database (Oxford)       Date:  2015-08-19       Impact factor: 3.451

10.  Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis.

Authors:  Brian A Klein; Tsute Chen; Jodie C Scott; Andrea L Koenigsberg; Margaret J Duncan; Linden T Hu
Journal:  Mob DNA       Date:  2015-10-06
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