Metadata-Version: 1.1
Name: prophyle
Version: 0.1.0.25
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
Description: 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 samtools=1.3.1
        	source activate prophyle
        	pip install --upgrade prophyle
        
        
        Environment activation::
        
        	source activate prophyle
        
        
        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::
        
        	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
        
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
