prophyle 0.1.0.19

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

Recommended way of installation using Conda

Environment installation:

conda create -y --name prophyle \
        -c etetoolkit -c bioconda \
        python==3.4 ete3 bitarray \
        parallel blast samtools=1.3.1

Environment activation:

source activate prophyle

Compile all programs:

make

Pipeline example

prophyle download bacteria prophyle index -t bacteria.nw -g bacteria/ idx_bacteria prophyle classify idx_bacteria reads.fq > result.sam