Metadata-Version: 2.0
Name: prophyle
Version: 0.1.0.21
Summary: ProPhyle metagenomic classifier
Home-page: https://github.com/karel-brinda/prophyle
Author: Karel Brinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov
Author-email: kbrinda@hsph.harvard.edu, salikhov.kamil@gmail.com, pignottisimone@gmail.com, gregory.kucherov@univ-mlv.fr
License: MIT
Keywords: metagenomics classification NGS
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: MIT License
Requires-Dist: bitarray
Requires-Dist: ete3
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: six
Requires-Dist: wheel

ProPhyle - accurate and resource-frugal phylogeny-based metagenomic classification
==================================================================================


.. image:: https://travis-ci.org/karel-brinda/prophyle.svg?branch=master
	:target: https://travis-ci.org/karel-brinda/prophyle

ProPhyle is a metagenomic classifier based on BWT-index and phylogenetic trees,
whose indexing strategy is based on the bottom-up propagation of genomes' k-mers in the tree,
assembling contigs at each node and matching using a standard full-text search.
The analysis of shared k-mers between NGS reads and the genomes in the index determines
which nodes are the best candidates for their classification.


Getting started
---------------


Prerequisities
^^^^^^^^^^^^^^

* GCC 4.8+
* ZLib
* Python 3 with ete3 library
* SamTools


Installation using Conda (recommended)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Environment installation::

	conda create -y --name prophyle \
		-c etetoolkit -c bioconda \
		python==3 ete3 bitarray \
		parallel blast samtools=1.3.1

	source activate prophyle

	pip install prophyle


Environment activation::

	source activate prophyle


Installation using PIP
^^^^^^^^^^^^^^^^^^^^^^

>From PyPI::

	pip install --upgrade prophyle

>From Git::

	git clone http://github.com/karel-brinda
	pip install --upgrade prophyle

>From PyPI to the current directory::

	export PYTHONUSERBASE=`pwd`
	pip install --user prophyle
	export PYTHONUSERBASE=`pwd`
	export PATH=$PATH:`pwd`/bin


Pipeline example
^^^^^^^^^^^^^^^^

Quick example::

	prophyle download bacteria
	prophyle index -k 10 ~/prophyle/test_bacteria.nw test_idx
	prophyle classify test_idx reads.fq > result.sam


