cnh/snapr

SNAPR: a bioinformatics pipeline for efficient and accurate RNA-seq alignment and analysis

SNAPR

Scalable Nucleotide Alignment Program RNA-seq - http://price.systemsbiology.net/SNAPR

Overview

We present SNAPR, a new method for RNA-seq analysis, optimized for hundreds or even thousands of RNA-seq libraries. SNAPR reads from and writes to BAM format, automatically generates read counts, and accurately identifies viral/bacterial infections and gene fusions.

Documentation

A quick start guide and user manual are available in the docs folder, with additional documentation at http://price.systemsbiology.net/SNAPR.

Building

SNAPR 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:

• g++ version 4.6
• zlib 1.2.8 from http://zlib.net/