Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

Arthur W. Pightling; Nicholas Petronella; Franco Pagotto

doi:10.1371/journal.pone.0104579

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Open Access

Peer-reviewed

Research Article

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

Arthur W. Pightling,

Affiliation Listeriosis Reference Service for Canada, Research Division, Bureau of Microbial Hazards, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
⨯
Nicholas Petronella,

Affiliation Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
⨯
Franco Pagotto

* E-mail: Franco.Pagotto@hc-sc.gc.ca

Affiliation Listeriosis Reference Service for Canada, Research Division, Bureau of Microbial Hazards, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
⨯

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

Arthur W. Pightling,
Nicholas Petronella,
Franco Pagotto

Published: August 21, 2014
https://doi.org/10.1371/journal.pone.0104579

About the Authors

Arthur W. Pightling

Affiliation Listeriosis Reference Service for Canada, Research Division, Bureau of Microbial Hazards, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada

Nicholas Petronella

Affiliation Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada

Franco Pagotto

* E-mail: Franco.Pagotto@hc-sc.gc.ca

Affiliation Listeriosis Reference Service for Canada, Research Division, Bureau of Microbial Hazards, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: AWP. Performed the experiments: NP. Analyzed the data: FP. Contributed to the writing of the manuscript: AWP.

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Sequence alignment
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Single nucleotide polymorphisms
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Listeria monocytogenes
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Nucleotide sequencing
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Genomics
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Biotechnology
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Phylogenetic analysis
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Archives
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