The Portable Microhaplotype Object and Tools

Area of Science:

• Genomics
• Bioinformatics
• Data Science

Background:

• The increasing volume of targeted sequencing data necessitates standardized formats for effective data management.
• Current data storage solutions are disparate, hindering data sharing, reuse, and the development of interoperable analysis tools.

Purpose of the Study:

• To introduce a standardized, efficient, and lossless format for storing phased targeted sequencing data (microhaplotypes).
• To facilitate data sharing, reuse, and the development of harmonized analysis tools in genomics research.

Main Methods:

• Development of the Portable Microhaplotype Object (PMO) format, a JSON-based standard for genetic data and metadata.
• Creation of pmotools-python, an open-source package for PMO data manipulation.
• Development of a web-based application for easy PMO file creation from tabular data.

Main Results:

• The PMO format provides efficient, relational storage of microhaplotype data with comprehensive metadata.
• The associated software tools and web app simplify PMO data creation and management.
• Demonstrated broad applicability across diverse organisms including *Plasmodium*, *Anopheles*, *Escherichia coli*, and *Staphylococcus aureus*.

Conclusions:

• The PMO format and associated tools offer a standardized solution for targeted sequencing data.
• PMO adoption will streamline data sharing, enhance interoperability, and accelerate genomic research.
• The project resources are openly available to promote widespread use and collaboration.