Gene

Biology

Transposable element

Computer science

Computational biology

Bacteriophage

Genetics

Genome

Source code

Escherichia coli

Prophage

Artificial intelligence

Programming language

Python (programming language)

Metagenomics

Annotation

Bioinformatics

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.

Phigaro: high-throughput prophage sequence annotation