TreeToReads statistics

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Citations per year

Number of citations per year for the bioinformatics software tool TreeToReads
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Tool usage distribution map

This map represents all the scientific publications referring to TreeToReads per scientific context
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Associated diseases

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Protocols

TreeToReads specifications

Information


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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Versioning


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Documentation


Maintainer


  • person_outline Emily Jane McTavish

Publication for TreeToReads

TreeToReads citation

call_split

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

2017
PeerJ
PMCID: 5782805
PMID: 29372115
DOI: 10.7717/peerj.3893
call_split See protocol

[…] ajor 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 can be r […]


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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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