GitHub - ablab/rectangles

This repository has been archived by the owner on Dec 23, 2019. It is now read-only.

Name		Name	Last commit message	Last commit date
Latest commit History 30 Commits
utils		utils
.gitignore		.gitignore
LICENSE		LICENSE
N50.py		N50.py
README		README
abstract_graph.py		abstract_graph.py
bigraph.py		bigraph.py
check_diags.py		check_diags.py
diagonal.py		diagonal.py
experimental.py		experimental.py
fastaparser.py		fastaparser.py
graph.py		graph.py
pathsets.py		pathsets.py
rectangle.py		rectangle.py
rectangle_set.py		rectangle_set.py
rrr.py		rrr.py
saveparser.py		saveparser.py
test_util.py		test_util.py
utils.py		utils.py

Repository files navigation

RECTANGLE GRAPH MODULE
======================

This module can be run on top of SPAdes [http://bioinf.spbau.ru/spades]
output directory to resolve repeats using information from paired-end reads.

Citation
========

Nikolay Vyahhi, Son K. Pham, Pavel Pevzner.
From de Bruijn Graphs to Rectangle Graphs for Genome Assembly,
Lecture Notes in Bioinformatics 7534 (2012), pp. 249-261.
http://www.springerlink.com/content/e617788h25u36440/

License
=======

Developed in Algorithmic Biology Lab of St. Petersburg Academic University
of the Russian Academy of Sciences.
See LICENSE file for details.

Requirements
============

Python 2.7.x (2.5 and 2.6 may also work)

Usage
=====

1. Run SPAdes in debug mode (spades.py --debug), so it will produce saves directory.
2. Run rectangle module by command line:
    python rrr.py -s project_name/saves [-o out_dir=out]
3. Check out_dir for contigs, log files and other interesting debug information.

Questions
=========

If you have any questions of comments, please email them to
Nikolay Vyahhi <vyahhi@bioinf.spbau.ru>

We'll be happy to hear your feedback.