Alview

Alview visualizes short-read sequencing alignments against reference genomes using SAM and BAM files to support inspection and analysis of alignment data.

Key Features:

• Alignment Visualization: Displays short-read sequence alignments mapped to reference genomes using SAM and BAM file formats.
• Multi-Mode Execution: Operates as a web server, command-line tool, and graphical application for viewing alignment data.
• Portable Implementation: Implements core functionality in portable C with optional graphical components developed in C, C++, and Objective-C.
• Cross-Platform Operation: Runs on Microsoft Windows, Linux, and Apple OS X environments for alignment analysis.

Scientific Applications:

• Alignment Quality Assessment: Examines read mapping accuracy and identifies potential sequencing or alignment errors.
• Variant Detection Support: Facilitates identification of genomic variants such as single nucleotide polymorphisms (SNPs) and structural variations through alignment inspection.
• Genomic Data Exploration: Enables detailed exploration of large-scale sequencing alignment datasets.

Methodology:

Alview reads short-read alignment data in SAM or BAM format alongside reference genome sequences and generates visual representations of the alignments for inspection and analysis.