PEPR: Pipelines for evaluating prokaryotic references

Nathan D. Olson; Justin M. Zook; Daniel V. Samarov; Scott A. Jackson; Marc L. Salit

doi:10.7287/peerj.preprints.1435v1

PEPR: Pipelines for evaluating prokaryotic references

Nathan D. Olson ¹, Justin M. Zook², Daniel V. Samarov³, Scott A. Jackson¹, Marc L. Salit^1,4

1 Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, United States

2 Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, United States

3 Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland, United States

4 Department of Bioengineering, Stanford University, Stanford, California, United States

DOI: 10.7287/peerj.preprints.1435v1

Published: 2015-10-15
Accepted: 2015-10-15

Subject Areas: Bioinformatics, Genomics, Microbiology
Keywords: microbiology, whole genome sequencing, bioinformatics

Copyright: © 2015 Olson et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Cite this article: Olson ND, Zook JM, Samarov DV, Jackson SA, Salit ML. 2015. PEPR: Pipelines for evaluating prokaryotic references. PeerJ PrePrints 3:e1435v1 https://doi.org/10.7287/peerj.preprints.1435v1

Abstract

The rapid adoption of microbial whole genome sequencing in public health, clinical testing, and forensic laboratories requires the use of validated measurement processes. Reference materials that are well characterized, homogeneous, and stable can be used to evaluate measurement processes and help to establish confidence in the results. Given the variety of microbial genome sequencing applications and platforms, as well as the vast microbial genomic diversity, there is a need for application-specific genomic materials for method validation. We have developed a reproducible and transparent bioinformatics tool for characterizing prokaryotic genomic materials; ”PEPR”, Pipelines for Evaluating Prokaryotic References. We demonstrate the tool and its output using sequencing data while developing a Staphylococcus aureus candidate genomic reference material.

Author Comment

We have developed a reproducibile and transparent bioinformatics tool for characterizing prokaryotic genomic materials; ”PEPR”, Pipelines for Evaluating Prokaryotic References.