ProPhyle metagenomic classifier
Project description
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
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