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The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets

Jason W. Sahl, Darrin Lemmer, Jason Travis, James M. Schupp, John D. Gillece, Maliha Aziz, Elizabeth M. Driebe, Kevin Drees, Nathan Hicks, Charles H.D. Williamson, Crystal Hepp, David Smith, Chandler Roe, David M. Engelthaler, David M. Wagner, Paul Keim
doi: https://doi.org/10.1101/037267
Jason W. Sahl
1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ
2Translational Genomics Research Institute, Flagstaff, AZ
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Darrin Lemmer
2Translational Genomics Research Institute, Flagstaff, AZ
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Jason Travis
2Translational Genomics Research Institute, Flagstaff, AZ
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James M. Schupp
2Translational Genomics Research Institute, Flagstaff, AZ
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John D. Gillece
2Translational Genomics Research Institute, Flagstaff, AZ
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Maliha Aziz
2Translational Genomics Research Institute, Flagstaff, AZ
3The George Washington University, Washington D.C.
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Elizabeth M. Driebe
2Translational Genomics Research Institute, Flagstaff, AZ
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Kevin Drees
1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ
4University of New Hampshire
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Nathan Hicks
2Translational Genomics Research Institute, Flagstaff, AZ
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Charles H.D. Williamson
1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ
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Crystal Hepp
1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ
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David Smith
2Translational Genomics Research Institute, Flagstaff, AZ
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Chandler Roe
2Translational Genomics Research Institute, Flagstaff, AZ
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David M. Engelthaler
2Translational Genomics Research Institute, Flagstaff, AZ
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David M. Wagner
1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ
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Paul Keim
1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ
2Translational Genomics Research Institute, Flagstaff, AZ
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Abstract

Whole genome sequencing (WGS) of bacteria is becoming standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. The Northern Arizona SNP Pipeline (NASP) was developed as a reproducible pipeline that scales well with the large amount of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares to other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces comparable, and often better, results to other pipelines, but is much more flexible in terms of data input types, job management systems, diversity of supported tools, and output formats. We also demonstrate differences in results based on the choice of the reference genome and choice of inferring phylogenies from concatenated SNPs or alignments including monomorphic positions. NASP represents a source-available, version-controlled, unit-tested method and can be obtained from tgennorth.github.io/NASP.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 25, 2016.
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The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets
Jason W. Sahl, Darrin Lemmer, Jason Travis, James M. Schupp, John D. Gillece, Maliha Aziz, Elizabeth M. Driebe, Kevin Drees, Nathan Hicks, Charles H.D. Williamson, Crystal Hepp, David Smith, Chandler Roe, David M. Engelthaler, David M. Wagner, Paul Keim
bioRxiv 037267; doi: https://doi.org/10.1101/037267
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The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets
Jason W. Sahl, Darrin Lemmer, Jason Travis, James M. Schupp, John D. Gillece, Maliha Aziz, Elizabeth M. Driebe, Kevin Drees, Nathan Hicks, Charles H.D. Williamson, Crystal Hepp, David Smith, Chandler Roe, David M. Engelthaler, David M. Wagner, Paul Keim
bioRxiv 037267; doi: https://doi.org/10.1101/037267

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