title: Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.
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.
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Richard P
authors.initials: RP
authors.lastname: Finney
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Qing-Rong
authors.initials: QR
authors.lastname: Chen
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Cu V
authors.initials: CV
authors.lastname: Nguyen
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Chih Hao
authors.initials: CH
authors.lastname: Hsu
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Chunhua
authors.initials: C
authors.lastname: Yan
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Massih
authors.initials: M
authors.lastname: Abawi
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Bian
authors.affiliation: Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
authors.forename: Daoud M
authors.initials: DM
authors.lastname: Meerzaman
keywords: BAM; alignment; genomics; open source; short read; visualization