Ragout
======

Version: 1.2

Release date: ?? Mar 2015

Website: http://fenderglass.github.io/Ragout/

[![Build Status](https://travis-ci.org/fenderglass/Ragout.svg?branch=master
)](https://travis-ci.org/fenderglass/Ragout)



       	         (
		     )    )
		  _.(--"("""--.._
		 /, _..-----).._,\
		|  `'''-----'''`  |
		 \               /
		  '.           .'
		    '--.....--'

Description
-----------
Ragout (Reference-Assisted Genome Ordering UTility)
is a tool for reference-assisted assembly using rearrangement approach. 
It takes initial sequences (a set of contigs/scaffolds) 
and a set of related references as input and produces a chromosome-scaled
assembly (as a set of gapped scaffolds).

Our approach involves the analysis of medium- and large-scale rearrangements
(like inversions or chromosomal translocations) between the input genomes
and finding most likely genomic structure for a target one. We also
try to make the assembly as complete as possible by using hierarchial
synteny structure as well as incorporating information from the assembly graph.
The first version of Ragout was limited to bacterial genomes only,
but currently there is an experimental support of mammalian-scaled ones.


Install
-------
See *docs/INSTALL.md* file.

Usage
-----
See *docs/USAGE.md* file.


Authors
-------
- Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of Sciences, UCSD)
- Pavel Avdeev (St. Petersburg University of the Russian Academy of Sciences)
- Dmitriy Meleshko (St. Petersburg University of the Russian Academy of Sciences)
- Son Pham (UCSD)


Citation
--------
- Mikhail Kolmogorov, Brian Raney, Benedict Paten, and Son Pham. 
"Ragout: A reference-assisted assembly tool for bacterial genomes",
Bioinformatics, 2014


ISMB 2014 supplementary
-----------------------

Supplementary materials for ISMB submission could be found at:
https://drive.google.com/file/d/0B1pUguR1yn7TMjNpX09JdFphT3c/edit?usp=sharing


Contacts
--------
Please report any problems directly to the github issue tracker.
Also, you can send your feedback to fenderglass@gmail.com


Acknowledgements
----------------
The work was partially supported by VP Foundation.

We would like to thank:
- Anna Liosnova (benchmarks and useful suggestions)
- Nikolay Vyahhi (testing and useful suggestions)
- Aleksey Gurevich (testing)


Third-party
-----------
Ragout package includes some third-patry software (see INSTALL.md for details)

* Networkx Python library [http://networkx.github.io/]
* Newick Python parser [http://www.daimi.au.dk/~mailund/newick.html]
* Sibelia [http://github.com/bioinf/Sibelia]


License
-------
Ragout itself is distributed under BSD license, but the package also contains
some third-party software. Most of this software is completely free to redistribute,
but some such as Sibelia or Newick parser are released under the GPL. We therefore release
Ragout distribution under the GPL and note that the licenses of the constituent
packages can be viewed in their subfolders. (see *LICENSE* file)