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Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
C++ C Other
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SNAPLib Fix up usage string to be more clear about stdin/stdout usage
apps 1.0beta.17: fix bug for very short FASTQ files
docs Allow hash table key size to vary and seed size to be up to 32
scripts * Multi-threaded read support for HDFS files. This required some changes
tests 1.0beta.13: Increase supplier queue size to avoid deadlock
.gitignore More 64 bit tweaking, plus include single or paired on the command li…
COPYING Changed to Apache 2 license
LICENSE Changed to Apache 2 license
Makefile 1.0dev.51: merge in changes from master, fix deadlock 0.16alpha.46


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:

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