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AmrPlusPlus specifications


Unique identifier OMICS_14218
Name AmrPlusPlus
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Input data A resistance database in the form of a FASTA file, a host/background genome in FASTA format for the removal of host/background contamination and a single or pair of FASTQ datasets
Input format FASTA
Output data A resistome counts, a rarefaction curves and read pair haplotypes
Operating system Unix/Linux, Mac OS
Programming languages C++
License MIT License
Computer skills Medium
Version 1.1
Stability Stable
Maintained Yes




No version available



  • person_outline Christina Boucher

Publication for AmrPlusPlus

AmrPlusPlus citation


Impact of sequencing depth on the characterization of the microbiome and resistome

Sci Rep
PMCID: 5897366
PMID: 29651035
DOI: 10.1038/s41598-018-24280-8
call_split See protocol

[…] xy Web server instance supported by the National Microbiology Laboratory, Public Health Agency of Canada (PHAC NML Galaxy). A custom workflow integrating Kraken taxonomic classification tools and the AmrPlusPlus resistome analysis pipeline tools was setup in Galaxy to obtain simultaneous outputs for both resistome and microbiome analyses of metagenomic sample reads from a single metagenome-resisto […]

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AmrPlusPlus institution(s)
Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA; Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA; Department of Computer Science, Colorado State University, Fort Collins, CO, USA; Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA; Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA
AmrPlusPlus funding source(s)
This work was supported by the Infectious Disease Supercluster and CSU Ventures at Colorado State University; Beef Checkoff; United States Department of Agriculture (2014-05257, 2015-03538) and the National Institutes of Health (5T32OD012201).

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