Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
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docs Allow hash table key size to vary and seed size to be up to 32 Sep 3, 2013
import remove proprietary files Sep 30, 2015
scripts * Multi-threaded read support for HDFS files. This required some changes Mar 21, 2014
tests propagate new name for SNAP: snap-aligner Sep 30, 2015
LICENSE Changed to Apache 2 license Oct 15, 2012
Makefile change linux binary name to snap-aligner Apr 29, 2015 0.16alpha.46 Nov 26, 2013
snap.sln 1.0dev.76: reduce allocation during sort phase May 1, 2015


Scalable Nucleotide Alignment Program -


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.


A quick start guide and user manual are available in the docs folder, with additional documentation at


SNAP runs on Windows, Linux and Mac OS X.

For Windows, we provide a Visual C++ project, snap.sln. Requirements:

  • Visual Studio 2012 (11.0)

For Linux and OS X, simply type make. Requirements: