.. SPID documentation master file, created by
   sphinx-quickstart on Wed Jun 24 16:09:13 2015.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. TODO revise this whole documentation

==================
SPID documentation
==================

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

SPID stands for "Sequences with Polymorphic Indices Demultiplexer"

SPID is a software for demultiplexing FASTQ files based on tags (a.k.a barcodes) which are attached to each sequence.

SPID was planned to enable users to use with a wide range of tag types, and to mix samples with different tag types
and different locations on the sequences, together in the same lane.

SPID reads multiplexed FASTQ files generated by bcl2fastq, Illumina's base calling and demultiplexing software,
and outputs demultiplexed FASTQ files in a similar format.

The source code can be downloaded from https://bitbucket.org/incpm/spid-public

Why use SPID?
=============

.. toctree::
    :maxdepth: 1

   features

Contents
========

.. toctree::
    :maxdepth: 2

    installation
    getting-started
    memory-usage
..
    Indices and tables
    ==================
    * :ref:`genindex`
    * :ref:`modindex`
    * :ref:`search`

License
=======
If not otherwise stated inside single files, SPID is licensed under GNU General Public License, version 3

Authors
=======
Refael Kohen,

refael.kohen@gmail.com

Ophir Tal,

ophir.tal@weizmann.ac.il

Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel.