Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
C++ C Other
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SNAPLib Merge branch 'master' of Jan 20, 2016
apps Disable daemon mode until the Linux version works Nov 15, 2014
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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
.gitignore change linux binary name to snap-aligner Apr 29, 2015
COPYING Changed to Apache 2 license Oct 15, 2012
Makefile 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: