multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

Area of Science:

• Bioinformatics
• Genomics
• Microbiology

Background:

• Phage annotation tools often lack scalability for high-throughput sequencing.
• Accurate functional assignment of phage genes is crucial for understanding phage biology and evolution.

Purpose of the Study:

• To develop an automated, scalable pipeline for high-throughput phage genome annotation.
• To improve the accuracy of gene calling and functional prediction in phage genomes.

Main Methods:

• Developed multiPhATE, a Python-based throughput pipeline driver invoking the PhAGE Annotation Toolkit and Evaluator (PhATE).
• Integrated a de novo phage gene calling algorithm and utilized phage-centric databases for functional assignment.
• Designed a modular pipeline allowing users to select specific analyses and local databases.

Main Results:

• Successfully demonstrated multiPhATE by annotating two novel *Yersinia pestis* phage genomes.
• The pipeline is adaptable for throughput sequencing projects, leveraging multi-processor implementation.
• multiPhATE provides comprehensive annotation, including de novo gene prediction and functional assignment.

Conclusions:

• multiPhATE offers an efficient and scalable solution for automated phage genome annotation.
• The tool enhances the analysis of large phage sequencing datasets, facilitating discoveries in phage biology.
• Open-source availability and modular design promote widespread adoption and customization.