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

Richard P Finney¹, Qing-Rong Chen¹, Cu V Nguyen¹

¹Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.

Cancer Informatics

|September 30, 2015

Summary

Alview is a versatile software tool designed for visualizing sequencing data alignments. It processes short-read sequences against reference genomes, offering flexible deployment as a web server, command-line tool, or GUI application.

Keywords:

BAM alignment genomics open source short read visualization

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Visualizing sequencing data alignments is crucial for genomic analysis.
Existing tools may lack flexibility or cross-platform compatibility.

Purpose of the Study:

To introduce Alview, a novel software tool for visualizing sequencing data alignments.
To provide a flexible and accessible solution for genomic data visualization.

Main Methods:

Alview processes Sequence Alignment Map (SAM) or Binary Alignment Map (BAM) files and reference genome data.
The software is written in portable C with optional C++, and Objective-C for the graphical user interface (GUI).
Alview supports execution as a web server, command-line tool, or native GUI application.

Main Results:

Alview generates visualizations of short-read sequences aligned to a reference genome.
The tool is compatible with Microsoft Windows, Linux, and Apple OS X operating systems.
A web demo and downloadable source code with executables are available.

Conclusions:

Alview offers a powerful and adaptable solution for visualizing sequencing alignment data.
Its cross-platform compatibility and multiple deployment options enhance accessibility for researchers.