phigaro 0.2.1.2.2

Phigaro is a scalable command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes) and is based on phage genes HMMs and a smoothing window algorithm.

Phigaro

Phigaro is a command-line tool for predictions phages and prophages from nucleid acid sequences (including metagenomes) and is based on phage genes HMMs (pVOG) and a smoothing window algorithm.

Requirements

Note, that in order to run Phigaro, you need to have Prodigal and HMMER installed. To install Prodigal, download it at https://github.com/hyattpd/Prodigal/wiki/installation and follow the instructions. To install HMMER, download it at http://hmmer.org/ Also note that you need locate to successfully run setup. It is pre-installed in the latest Ubuntu distributions, but in case you don't have it, please run sudo apt-get install locate, it is a very useful tool.

Installation

sudo -H pip3 install phigaro

then create a config file with:

phigaro-setup

It may take some time, since we are downloading the database

Usage

phigaro -h                                                                                                                                                                          15:04:32
usage: phigaro [-h] [-V] -f FASTA_FILE [-c CONFIG] [-p] [-e EXTENSION [EXTENSION ...]] [-o OUTPUT] [--not-open] [-t THREADS]

optional arguments:
  -h, --help            show this help message and exit
  -f FASTA_FILE, --fasta-file FASTA_FILE
                        Assembly scaffolds\contigs or full genomes
  -c CONFIG, --config CONFIG
                        config file
  -v, --verbose
  -t THREADS, --threads THREADS
                        num of threads (default is num of CPUs)
  -o, --output OUTPUT 
                        output filename for html and txt outputs. Required by default, but not required for stdout only output
  -p, --print-vogs
                        print phage vogs for each region
  --no-html 
                        do not generate output html file
  --not-open 
                        do not open automatically html file
  -e, --extension
                        type of the output: html, txt or stdout. Default is html. You can specify several file formats with a space as a separator. Example: -e txt html stdout
  --not-open
                        do not open html file automatically, if html output type is specified

Running time depends on the size of your input data and the number of CPUs used. The approximate running time for a metagenomic assembly file of 150MB is about 20 minutes.

Output

The output can be on html, text or stdout format.

Modus operandi

ORFs and corresponging proteins are predicted from the input .fasta file using Prodigal. Phage genes are predicted with pVOG Hidden Markov Models that can be downloaded stand-alone from http://dmk-brain.ecn.uiowa.edu/pVOGs/. Each contig is represented as a sequence of phage and non-phage genes. A smoothing window algorithm determines regions with high density of phage genes and prophage boundaries.

In case of any questions regarding installing and running Phigaro, please, adress [e-mail]

(c) E.Starikova, P. Tikhonova, N.Pryanichnikov, 2019