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

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 structura...

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Detalles Bibliográficos
Autores principales: Carver, Tim, Böhme, Ulrike, Otto, Thomas D., Parkhill, Julian, Berriman, Matthew
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828118/
https://www.ncbi.nlm.nih.gov/pubmed/20071372
http://dx.doi.org/10.1093/bioinformatics/btq010
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author Carver, Tim
Böhme, Ulrike
Otto, Thomas D.
Parkhill, Julian
Berriman, Matthew
author_facet Carver, Tim
Böhme, Ulrike
Otto, Thomas D.
Parkhill, Julian
Berriman, Matthew
author_sort Carver, Tim
collection PubMed
description 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
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spelling pubmed-28281182010-02-25 BamView: viewing mapped read alignment data in the context of the reference sequence Carver, Tim Böhme, Ulrike Otto, Thomas D. Parkhill, Julian Berriman, Matthew Bioinformatics Applications Note 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 Oxford University Press 2010-03-01 2010-01-12 /pmc/articles/PMC2828118/ /pubmed/20071372 http://dx.doi.org/10.1093/bioinformatics/btq010 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Carver, Tim
Böhme, Ulrike
Otto, Thomas D.
Parkhill, Julian
Berriman, Matthew
BamView: viewing mapped read alignment data in the context of the reference sequence
title BamView: viewing mapped read alignment data in the context of the reference sequence
title_full BamView: viewing mapped read alignment data in the context of the reference sequence
title_fullStr BamView: viewing mapped read alignment data in the context of the reference sequence
title_full_unstemmed BamView: viewing mapped read alignment data in the context of the reference sequence
title_short BamView: viewing mapped read alignment data in the context of the reference sequence
title_sort bamview: viewing mapped read alignment data in the context of the reference sequence
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828118/
https://www.ncbi.nlm.nih.gov/pubmed/20071372
http://dx.doi.org/10.1093/bioinformatics/btq010
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