title: PEPR: pipelines for evaluating prokaryotic references.
abstract: The rapid adoption of microbial whole genome sequencing in public health, clinical testing, and forensic laboratories requires the use of validated measurement processes. Well-characterized, homogeneous, and stable microbial genomic reference materials can be used to evaluate measurement processes, improving confidence in microbial whole genome sequencing results. We have developed a reproducible and transparent bioinformatics tool, PEPR, Pipelines for Evaluating Prokaryotic References, for characterizing the reference genome of prokaryotic genomic materials. PEPR evaluates the quality, purity, and homogeneity of the reference material genome, and purity of the genomic material. The quality of the genome is evaluated using high coverage paired-end sequence data; coverage, paired-end read size and direction, as well as soft-clipping rates, are used to identify mis-assemblies. The homogeneity and purity of the material relative to the reference genome are characterized by comparing base calls from replicate datasets generated using multiple sequencing technologies. Genomic purity of the material is assessed by checking for DNA contaminants. We demonstrate the tool and its output using sequencing data while developing a Staphylococcus aureus candidate genomic reference material. PEPR is open source and available at https://github.com/usnistgov/pepr .
authors.affiliation: Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA. nolson@nist.gov.
authors.forename: Nathan D
authors.identifier: http://orcid.org/0000-0003-2585-3037
authors.initials: ND
authors.lastname: Olson
authors.affiliation: Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
authors.forename: Justin M
authors.initials: JM
authors.lastname: Zook
authors.affiliation: Statistical Engineering Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
authors.forename: Daniel V
authors.initials: DV
authors.lastname: Samarov
authors.affiliation: Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.|Department of Bioengineering, Stanford University, Stanford, CA, USA.
authors.forename: Marc L
authors.initials: ML
authors.lastname: Salit
mesh_terms: D019295:Computational Biology; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing
keywords: Bioinformatics; Microbiology; Whole genome sequencing