NIST Microbial Genomic Reference Materials

Characterization of Bacterial Genomic Reference Materials

Nathan D. OlsonNational Institute of Standards and Technology

Biosystems and Biomaterials Bioforum October 2015

Opinions expressed in this paper are the authors and do not necessarily reflect the policies and views of NIST or affiliated venues. Certain commercial equipment, instruments, or materials are identified in this paper only to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by the NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Official contribution of NIST; not subject to copyrights in USA.

NIST Microbial Genomic Reference Materials

Why Bacterial Genomic RMs?

Background Material Selection Characterization

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Quality Control

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RM Selection

Background Material Selection Characterization

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Material Selection and Acquisition

Strain Selection

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RM Characterization

Background Material Selection Characterization

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Background Material Selection Characterization

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Background Material Selection Characterization

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Background Material Selection Characterization

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Background Material Selection Characterization

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Background Material Selection Characterization

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Background Material Selection Characterization

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Background Material Selection Characterization

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Background Material Selection Characterization

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Pipeline for Evaluating Prokaryotic References

Background Material Selection Characterization

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● S. enterica and S. aureus preliminary results○ Characterization of Bacterial Genomic Reference Materials.

■ http://dx.doi.org/10.6084/m9.figshare.1451417

● Bioinformatic Pipeline ○ Manuscript Pre-Print Coming Soon https://peerj.com/preprints/

Characterization Results

Background Material Selection Characterization

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Computational ReproducibilityCode EnvironmentData

Background Material Selection Characterization

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Computational ReproducibilityData

● Sequence data NIH SRA ○ Bioproject PRJNA252728 http://www.ncbi.nlm.nih.

gov/bioproject/PRJNA252728 ● Optical Mapping and Genome Assembly

○ https://github.com/nate-d-olson/NIST_Micro_Genomic_RM_Data

Background Material Selection Characterization

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Computational Reproducibility

● Bioinformatic Pipeline ○ https://github.com/usnistgov/pepr

○ https://hub.docker.com/r/natedolson/pepr/

○ https://hub.docker.com/r/natedolson/docker-pathoscope/

● Data Analysis and Reporting○ https://github.com/usnistgov/peprr

Code

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Conclusions● Microbial genomic RMs characterized:

○ Genome Assembly○ Base Level Purity○ Genomic Contaminants

● RMs and associated data will help validate sequencing and bioinformatic processes.

● Reproducible and transparent characterization

NIST Microbial Genomic Reference Materials

AcknowledgementsFDA:○ Heike Sichtig○ Marc Allard○ Tim Muruvanda○ Shashi Sharma○ Nagarajan Thirunavukkarasu

NIST:○ Marc Salit○ Justin Zook○ Scott Jackson○ Nancy Lin○ Jenny McDaniel○ Lindsay Vang○ David Catoe○ Steven Lund

This work was supported by the Department of Homeland Security (DHS) Science and Technology Directorate under the Interagency Agreement HSHQPM-12-X-00078 with NIST and by two interagency agreements with the FDA.