ProPhyle metagenomic classifier
Project description
ProPhyle is a metagenomic classifier based on BWT-index and phylogenetic trees. The indexing strategy is based on the 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.
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 Conda
Environment installation:
conda create -y --name prophyle -c etetoolkit -c bioconda \
python==3.6 ete3 bitarray samtools=1.3.1
source activate prophyle
pip install --upgrade prophyle
Environment activation:
source activate prophyle
Examples
Quick example (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
Quick example (k=31, full bacterial database):
prophyle download bacteria prophyle index -k 31 ~/prophyle/bacteria.nw test_idx prophyle classify test_idx reads.fq > result.sam
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