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Review
. 2015 Sep 13:14:105-7.
doi: 10.4137/CIN.S26470. eCollection 2015.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

Richard P Finney  1 , Qing-Rong Chen  1 , Cu V Nguyen  1 , Chih Hao Hsu  1 , Chunhua Yan  1 , Ying Hu  1 , Massih Abawi  1 , Xiaopeng Bian  1 , Daoud M Meerzaman  1
Affiliations
Review

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

Richard P Finney et al. Cancer Inform. .

Abstract

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

Keywords: BAM; alignment; genomics; open source; short read; visualization.

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Figures

Figure 1
Figure 1
Information and navigation in Alview – upper left is original and lower right is zoom in via mouse drag to examine SNP. Various navigation buttons and information blocks assist in browsing BAM files.
See this image and copyright information in PMC

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