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==3.6 ete3 bitarray samtools=1.3.1 source activate prophyle pip install --upgrade prophyle
Environment activation:
source activate prophyle
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
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
prophyle-0.1.0.28.tar.gz
(2.8 MB
view hashes)
Built Distribution
Close
Hashes for prophyle-0.1.0.28-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4c47b33d45d095e483211efc9087d66fcbf9d28d1b6ff7b22b5ba44b106617b7 |
|
MD5 | e6aa7301a92a581fa10869ad413e9ced |
|
BLAKE2b-256 | d6493cd97478895a3c8b8a4fb68b8f45744b91bc6688cc6b1f9540e98316ecd4 |