MapView: visualization of short reads alignment on desktop computer
Overview:
MapView is an information-rich short reads alignment viewer with genetic detection capability for next-generation sequencing technologies. MapView supports a compact alignment view for both single-end and pair-end short reads, multiple navigation and zoom modes, and multi-thread processing. It can handle large-scale data with super-high computational efficiency. Moreover, MapView offers automated genetic variation detection.
Computational efficiency:
The great majority of alignment viewers were designed for loading and processing big assembly file in the ACE format. This memory based design requires huge amount of memory (>10G) not typically available to desktop computer users. MapView converts the reference file and alignment result file to a single file in the MapView format (MVF). The MVF binary format, combined with effective compressing and indexing of the aligned reads, will enable reduction in disk usage and quick positioning. MapView is a disk based viewer and it only loads displayed section of the MVF file into memory. MapView¡¯s file handling is designed to prevent it from using all the available memory. This leads to a small burden on memory resources (<60M) while not compromising the speed (<2s).
Please cite : MapView: visualization of short reads alignment on a desktop computer. Bioinformatics, 2009, 25 (12) : 1554-1555
Download:
MapView 3.4.1 (For Windows and Linux)
If .Net Framwork is not installed on your Windows system, you need to install 32 bit .NET Framwork 2.0 or 64 bit NET Framwork 2.0 according to your computer system.
You can also run MapView on Linux system (e.g. Ubuntu) using Mono (http://www.mono-project.com/).
Test datasets:
1.Example datasets
Small example data readme
Pair-end example data readme
2.Datasets for efficiency tests
43,596,771 bp reference and 6,615,627 Illumina 44bp reads readme
43,596,771 bp reference and 26,531,161 Illumina 44bp reads readme
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