
Introduction
============

What is Scalpel?
----------------

Scalpel is a DNA micro-assembly pipeline for detecting 
INDEL (INsertion and DEletion) mutations in Next-Generation Sequencing (NGS) data.

What does it mean that Scalpel is in "beta"?
--------------------------------------------

Scalpel is currently under active development and it will be likely to see
changes in the output and command line parameters in the near future.

Obtaining Scalpel
=================

Scalpel can be downloaded from the Sourceforge site at the following address:

http://sourceforge.net/projects/scalpel/

The package has been tested under Linux and Mac OS X operating systems.

Building from source
--------------------

Building and running Scalpel from source requires a GNU-like environment with 

1. GCC
2. GNU Make
3. GNU CMake
4. Perl 5.10 or later

It should be possible to build Scalpel on most Linux installations 
or on a Mac installation with [Xcode and Xcode command line tools] installed.

Instructions to install Xcode (Mac only): 
(1) install Xcode
(2) open XCode -> Preferences -> Downloads -> Download XCode Command Line Tools [needed for 'make']

First, download the source package from the sourceforge site. 
Unzip the file, change to the unzipped directory, and build the
scalpel by running GNU `make` (usually with the command `make`, but
sometimes with `gmake`) with no arguments.  

Adding to PATH
--------------

By adding your Scalpel directory to your PATH (environment variable), you
ensure that whenever you run `scalpel` from the command line, you will get 
the version you just installed without having to specify the entire path.  
This is recommended for most users.  To do this, follow your operating system's 
instructions for adding the directory to your PATH.

Memory requirements
-------------------

For the human genome, a minimum of 3GB of RAM is required to run Scalpel. 
However, a machine with 10GB of RAM is recommended.

Documentation
=============

See included file MANUAL for details.

Wrapper
-------

The `scalpel-discovery` and `scalpel-export` executables are a Perl wrapper script that orchestrate 
the pipeline analysis. It is recommended that you always run the them directly.

License
=======

Scalpel is released under the MIT License.
Copyright (c) 2013-2014 Giuseppe Narzisi and Michael C. Schatz

See included file LICENSE for details.

Contact
======

If you have questions, comments, suggestions, bug reports, etc.
please send them to:

Giuseppe Narzisi 
New York Genome Center
Email: gnarzisi@nygenome.org
Project Website: http://sourceforge.net/projects/scalpel/

