prophyle 0.1.0.24

ProPhyle metagenomic classifier

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