prophyle 0.1.0.31

ProPhyle metagenomic classifier

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.

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