Metadata-Version: 2.0
Name: prophyle
Version: 0.1.0.31
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: psutil
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.
Its indexing strategy uses a bottom-up propagation of 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.

More information can be found in our `poster <http://brinda.cz/publications/2017_cmda_prophyle.pdf>`_.


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

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

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



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

>From PyPI::

	pip install --upgrade prophyle

>From Git::

	pip install --upgrade git+https://github.com/karel-brinda/prophyle

>From PyPI to the current directory::

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


Installation using Bioconda
^^^^^^^^^^^^^^^^^^^^^^^^^^^

Environment installation::

	conda create -c bioconda -n prophyle prophyle

Environment activation::

	source activate prophyle


Examples
^^^^^^^^

Quick test (small k, subsampled bacterial database)::

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

Bacterial database (k=31)::

	prophyle download bacteria
	prophyle index -k 31 ~/prophyle/bacteria.nw idx_bac
	prophyle classify idx_bac reads.fq > result.sam

Bacterial and viral database (k=31)::

	prophyle download bacteria
	prophyle download viruses
	prophyle index -k 31 ~/prophyle/bacteria.nw ~/prophyle/viruses.nw idx_bac_vir
	prophyle classify idx_bac_vir reads.fq > result.sam


