Scalable Nucleotide Alignment Program - https://www.microsoft.com/en-us/research/project/snap/
SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.
It also includes support for sorting, marking duplicates and indexing its results, eliminating the need for several pipeline stages used by other aligners.
The SNAP executable
The SNAPCommand tool
SNAP has a one page Quick Start Guide and a more extensive Manual.
SNAP runs on Windows, Linux and OSX.
For Windows, we provide a Visual C++ solution, snap.sln. Requirements:
When you build it, you will have to set it to build for x64, not "Any CPU" or 32 bit.
For Linux, simply type make. Requirements: