Phage Genome Annotation: Where to Begin and End.

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Renewed interest in phage research and accessible sequencing technologies are increasing the number of sequenced phage genomes.
• A growing need exists for efficient and reliable methods for phage genome assembly and annotation.
• Navigating the multitude of available tools for phage genome analysis can be challenging for new researchers.

Purpose of the Study:

• To provide a comprehensive overview of phage genome assembly and annotation processes.
• To guide researchers, particularly novices, through the steps from raw sequencing reads to genome submission.
• To highlight open-access tools and reproducible workflows for phage genome analysis.

Main Methods:

• Overview of the end-to-end process of phage genome assembly and annotation.
• Demonstration using worked examples for clarity.
• Focus on open-access bioinformatics tools and their integration into repeatable workflows.

Main Results:

• A guided pathway for phage genome assembly and annotation is presented.
• Multiple open-access tools are showcased for various stages of the process.
• Common pitfalls and challenges in phage genome analysis are identified and discussed.

Conclusions:

• This resource simplifies phage genome assembly and annotation for new researchers.
• The use of open-access tools promotes reproducibility and accessibility in phage genomics.
• A clear pathway to genome submission is provided, addressing a critical need in the field.