Visualizing next-generation sequencing data with JBrowse

Briefings in Bioinformatics

Volumn 14, Issue 2, 2013, Pages 172-177

  Westesson, Oscar ^a   Skinner, Mitchell ^a   Holmes, Ian ^a  

^a University of California at Berkeley   (United States)

Author keywords

Genome browser; Next generation sequencing; Web

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC DATABASE; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; STATISTICS;

COMPUTATIONAL BIOLOGY; DATA DISPLAY; DATABASES, GENETIC; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84875582766     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr078     Document Type: Article

References (18)

1. Skinner ME, Uzilov AV, Stein LD, et al. JBrowse: a next-generation genome browser. Genome Res 2009;19: 1630-8.
2. FASTA format. http://en.wikipedia.org/wiki/FASTA. 24 December 2011, date last accessed
3. BED format. http://genome.ucsc.edu/FAQ/FAQformat.html. 24 December 2011, date last accessed
4. GFF format. http://www.sanger.ac.uk/resources/software/gff/. 24 December 2011, date last accessed
5. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078-9.
6. WIG format. http://genome.ucsc.edu/goldenPath/help/wiggle.html. 24 December 2011, date last accessed.
7. Zhou P, Emmert D, Zhang P. Using Chado to store genome annotation data. Curr Protoc Bioinformatics 2006; Chapter 9:Unit 9.6.
8. Mungall CJ, Emmert DB. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics 2007;23:i337-46.
9. Stajich JE, Block D, Boulez K, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002;12: 1611-8.
10. Lister R, O'Malley RC, Tonti-Filippini J, etal. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008;133:523-36.
11. Down T, Piipari M, Hubbard T. Dalliance: interactive genome viewing on the web. Bioinformatics 2011;27:889.
12. Perlin K, Fox D. Pad: an alternative approach to the computer interface. Proceedings of the 20th Annual Conference on Computer Graphics and Interactive Techniques. Anaheim, CA, USA: ACM, 1993;57-64.
13. Alekseyenko A, Lee C. Nested containment list (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics 2007;23: 1386-93.
14. Kircher M. Lazy Acquisition. Munich, Germany: Siemens AG, 2001, pp. 1-11.
15. Stein L, Mungall C, Shu S, et al. The generic genome browser: a building block for a model organism system database. Genome Res 2002;12:1599-610.
16. Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res 2003;12:996-1006.
17. Stalker J, Gibbins B, Meid P, et al. The Ensembl web site: Mechanics of a genome browser. Genome Res 2004;14: 951-5.
18. Jenkinson A, Albrecht M, Birney E, et al. Integrating biological data-the Distributed Annotation System. BMC Bioinformatics 2008;9(Suppl 8):S3.