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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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PEPR: pipelines for evaluating prokaryotic references.

Nathan D Olson¹, Justin M Zook², Daniel V Samarov³

¹Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA. nolson@nist.gov.

Analytical and Bioanalytical Chemistry

|March 4, 2016

Summary

This summary is machine-generated.

A new bioinformatics tool, PEPR (Pipelines for Evaluating Prokaryotic References), ensures the quality and purity of microbial genomic reference materials. This enhances the reliability of microbial whole genome sequencing for public health and clinical applications.

Keywords:

Bioinformatics Microbiology Whole genome sequencing

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Area of Science:

Bioinformatics
Genomics
Microbiology

Background:

Microbial whole genome sequencing (WGS) adoption in public health, clinical testing, and forensics necessitates validated measurement processes.
Well-characterized genomic reference materials are crucial for evaluating WGS processes and increasing result confidence.

Purpose of the Study:

To develop a reproducible and transparent bioinformatics tool, PEPR, for characterizing prokaryotic genomic reference materials.
To evaluate the quality, purity, and homogeneity of reference genomes and the purity of genomic materials.

Main Methods:

PEPR assesses genome quality using high-coverage paired-end sequencing data, analyzing coverage, read size/direction, and soft-clipping rates to detect mis-assemblies.
Material homogeneity and purity are determined by comparing base calls from replicate datasets generated via multiple sequencing technologies.
Genomic purity is further assessed by identifying DNA contaminants.

Main Results:

The study demonstrates PEPR's utility in characterizing a Staphylococcus aureus candidate genomic reference material.
PEPR successfully evaluates genome quality, material homogeneity, and purity.

Conclusions:

PEPR provides a robust, open-source solution for characterizing microbial genomic reference materials.
The tool enhances confidence in microbial WGS results by ensuring the quality of reference materials.