Phigaro: high-throughput prophage sequence annotation

Elizaveta V Starikova; Polina O Tikhonova; Nikita A Prianichnikov; Chris M Rands; Evgeny M Zdobnov; Elena N Ilina; Vadim M Govorun

doi:10.1093/bioinformatics/btaa250

Phigaro: high-throughput prophage sequence annotation

Bioinformatics. 2020 Jun 1;36(12):3882-3884. doi: 10.1093/bioinformatics/btaa250.

Authors

Elizaveta V Starikova¹, Polina O Tikhonova¹, Nikita A Prianichnikov¹, Chris M Rands², Evgeny M Zdobnov², Elena N Ilina¹, Vadim M Govorun¹

Affiliations

¹ Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia.
² Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva 1206, Switzerland.

PMID: 32311023
DOI: 10.1093/bioinformatics/btaa250

Abstract

Summary: Phigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated 'prophage genome maps' and marks possible transposon insertion spots inside prophages. It is applicable for mining prophage regions from large metagenomic datasets.

Availability and implementation: Source code for Phigaro is freely available for download at https://github.com/bobeobibo/phigaro along with test data. The code is written in Python.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

High-Throughput Nucleotide Sequencing*
Metagenome
Metagenomics
Prophages* / genetics
Software