PEPR specifications


Unique identifier OMICS_12029
Name Pipelines for Evaluating Prokaryotic References
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Output data PEPR outputs include a corrected reference genome assembly, genome positions with high and low purity based on biological and technical variation, base level homogeneity of the material, as well as the percentage and identity of genus level genomic contaminants. The resulting characterization values are intentionally conservative and without uncertainty or confidence estimates, as sources of bias and error associated with the measurement process are currently not fully understood.
Biological technology Illumina, Life Technologies, Pacific Biosciences
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Nathan D. Olson <>

PEPR article

PEPR institution(s)
Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA; Statistical Engineering Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA
PEPR funding source(s)
Department of Homeland Security (DHS) Science and Technology Directorate funded this project under Interagency Agreement HSHQPM-14-X-00078 with NIST. This work was additionally supported by two interagency agreements between NIST and the FDA.

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