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.
Project description
Phigaro v 0.2.1.8
Phigaro is a command-line tool for predicting and annotating phages and prophages from nucleid acid sequences (including metagenome assemblies) and is based on identifying phage genes via pVOG profile HMMs and a smoothing window algorithm. https://doi.org/10.1101/598243
Requirements
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/.
You also need locate
. It is pre-installed in the latest Ubuntu distributions, but in case you don't have it, please run sudo apt-get install locate
.
Installation
sudo -H pip3 install phigaro
then create a config file with:
phigaro-setup
It may take some time, since you are downloading the databases.
Permissions
By default, root permissions are required for the installation. But you can disable it by adding a flag to '''phigaro-setup''':
phigaro-setup --no-updatedb
Moreover, you may want to change a path of a config installation file r reconfigurate ypur Phigaro - these can be also done by adding special flags:
phigaro-setup --help
usage: phigaro-setup [-h] [-c CONFIG] [-p PVOG] [-f] [--no-updatedb]
Phigaro setup helper
optional arguments:
-h, --help show this help message and exit
-c CONFIG, --config CONFIG
Path to a config.yml, default is
/home/polly/.phigaro/config.yml (default:
/home/polly/.phigaro/config.yml)
-p PVOG, --pvog PVOG pvogs directory, default is /home/polly/.phigaro/pvog
(default: /home/polly/.phigaro/pvog)
-f, --force Force configuration and rewrite config.yml if exists
(default: False)
--no-updatedb Do not run sudo updatedb (default: False)
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 running time for a metagenomic assembly file of 150MB is about 20 minutes.
Output
The output can be annotated prophage genome maps (html) or tabular format (text or stdout).
Test data
Test data is available in test_data
folder.
In order to run Phigaro on test data, enter the following command from your Phigaro folder:
phigaro -f test_data/Bacillus_anthracis_str_ames.fna -o test_data/Bacillus_anthracis_str_ames.phg -p --not-open
This command generates Bacillus_anthracis_str_ames.phg
and Bacillus_anthracis_str_ames.phg.html
files in test_data
folder.
If output file is not specified with -o
, the following output is generated:
scaffold begin end taxonomy
NC_003997.3 451613 457261 Siphoviridae
NC_003997.3 460328 482139 Siphoviridae
NC_003997.3 3460450 3482979 Siphoviridae
NC_003997.3 3495703 3505502 Siphoviridae
NC_003997.3 3749518 3776811 Siphoviridae
NC_003997.3 3779698 3784171 Siphoviridae
Methods overview
Open-reading frames (i.e. proteins) are predicted from the input FASTA file using Prodigal. Phage genes are annotated with prokaryotic viral orthologous groups (pVOGs) profile Hidden Markov Models (HMMs), which 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 (a triangular window function) determines regions with a high density of phage genes and therefore the prophage regions and boundaries, considering the pVOG annotations and the GC content.
Known issues
Phigaro is tested on Linux systems. For MacOS, you may need to add the following softlink ln -s /usr/libexec/locate.updatedb /usr/local/bin/updated
and run brew install wget
. If you encounter any issues while running Phigaro on test data, please report them to us at estarikova@rcpcm.org.
Publication
Elizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Vadim M. Govorun (2019), Phigaro: high throughput prophage sequence annotation, bioRxiv 598243; doi: https://doi.org/10.1101/598243
(c) E.Starikova, P. Tikhonova, N.Pryanichnikov, 2019
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