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
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
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