Journal Article

BamView: viewing mapped read alignment data in the context of the reference sequence

Tim Carver, Ulrike Böhme, Thomas D. Otto, Julian Parkhill and Matthew Berriman

in Bioinformatics

Volume 26, issue 5, pages 676-677
Published in print March 2010 | ISSN: 1367-4803
Published online January 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq010

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Summary: BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence. It supports the BAM (Binary Alignment/Map) format. It can be used in a number of contexts including SNP calling and structural annotation. BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features.

Availability: BamView and Artemis are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at: http://bamview.sourceforge.net/

Contact: artemis@sanger.ac.uk

Journal Article.  1352 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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