TreeToReads statistics

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Associated diseases

Associated diseases

TreeToReads specifications


Unique identifier OMICS_16993
Name TreeToReads
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Emily Jane McTavish <>

Publication for TreeToReads

TreeToReads in publication

PMCID: 5782805
PMID: 29372115
DOI: 10.7717/peerj.3893

[…] foodborne bacterial pathogens (l. monocytogenes, s. enterica ser. bareilly, e. coli, and c. jejuni) and one simulated dataset generated from the s. enterica ser. bareilly tree using the pipeline treetoreads (), for which both the true tree and snp positions are known. in addition, we propose a standard spreadsheet format for describing these and future benchmark datasets. that format […]

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TreeToReads institution(s)
University of California, Merced, Merced, CA, USA; University of Kansas, Lawrence, KS, USA; Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
TreeToReads funding source(s)
Supported by the Oak Ridge Institute for Science and Education (ORISE).

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