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NanoARG: A web service for identification of antimicrobial resistance elements from nanopore-derived environmental metagenomes

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Asymptomatic People May Contribute to Dengue Transmission

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WHO Survey Reveals Misconceptions About Antibiotic Resistance

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Occurrence and abundance of tetracycline, sulfonamide resistance genes, and class 1 integron in five wastewater treatment plants

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[5] Rapid and sensitive sequence comparison with FASTP and FASTA

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Assessing the performance of the Oxford Nanopore Technologies MinION

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Antibiotics and antibiotic resistance in water environments

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Antibiotic resistance in the environment: a link to the clinic?

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Analysis of the bacterial community in a laboratory-scale nitrification reactor and a wastewater treatment plant by 454-pyrosequencing

inferredcites →https://doi.org/10.1016/j.watres.2017.07.002openalex-snapshot

Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements

inferredcites →https://doi.org/10.1021/acs.est.5b03522openalex-snapshot

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

inferredcites →https://doi.org/10.1038/ismej.2013.189openalex-snapshot

Quantitative and qualitative impact of hospital effluent on dissemination of the integron pool

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Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

inferredcites →https://doi.org/10.1038/ismej.2015.59openalex-snapshot

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

inferredcites →https://doi.org/10.1038/ismej.2016.155openalex-snapshot

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection

inferredcites →https://doi.org/10.1038/nature08821openalex-snapshot

A human gut microbial gene catalogue established by metagenomic sequencing

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Bacterial phylogeny structures soil resistomes across habitats

inferredcites →https://doi.org/10.1038/nature17672openalex-snapshot

Interconnected microbiomes and resistomes in low-income human habitats

inferredcites →https://doi.org/10.1038/nbt.2862openalex-snapshot

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

inferredcites →https://doi.org/10.1038/nbt.3103openalex-snapshot

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

inferredcites →https://doi.org/10.1038/ncomms10063openalex-snapshot

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

inferredcites →https://doi.org/10.1038/ncomms11307openalex-snapshot

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot

A complete bacterial genome assembled de novo using only nanopore sequencing data

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

inferredcites →https://doi.org/10.1038/nrmicro2312openalex-snapshot

Call of the wild: antibiotic resistance genes in natural environments

inferredcites →https://doi.org/10.1038/srep38432openalex-snapshot

Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes

inferredcites →https://doi.org/10.1073/pnas.122108599openalex-snapshot

The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA)

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bib/bbs033openalex-snapshot

Functional assignment of metagenomic data: challenges and applications

inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btm451openalex-snapshot

Extending assembly of short DNA sequences to handle error

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/bts174openalex-snapshot

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

inferredcites →https://doi.org/10.1093/bioinformatics/btu555openalex-snapshot

Poretools: a toolkit for analyzing nanopore sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv557openalex-snapshot

Cytoscape.js: a graph theory library for visualisation and analysis

inferredcites →https://doi.org/10.1093/bioinformatics/btw136openalex-snapshot

ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database

inferredcites →https://doi.org/10.1093/bioinformatics/btw569openalex-snapshot

Nanocall: an open source basecaller for Oxford Nanopore sequencing data

inferredcites →https://doi.org/10.1093/jac/dkv206openalex-snapshot

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

inferredcites →https://doi.org/10.1093/jac/dkw397openalex-snapshot

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

inferredcites →https://doi.org/10.1093/nar/gks678openalex-snapshot

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

inferredcites →https://doi.org/10.1093/nar/gkt1252openalex-snapshot

BacMet: antibacterial biocide and metal resistance genes database

inferredcites →https://doi.org/10.1093/nar/gkw1328openalex-snapshot

Rapid resistome mapping using nanopore sequencing

inferredcites →https://doi.org/10.1099/jmm.0.052555-0openalex-snapshot

Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance

inferredcites →https://doi.org/10.1101/019281openalex-snapshot

Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION

inferredcites →https://doi.org/10.1101/gr.210641.116openalex-snapshot

Centrifuge: rapid and sensitive classification of metagenomic sequences

inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot

Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation

inferredcites →https://doi.org/10.1111/1755-0998.12324openalex-snapshot

A first look at the Oxford Nanopore MinION sequencer

inferredcites →https://doi.org/10.1111/j.1574-6976.2011.00273.xopenalex-snapshot

Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens

inferredcites →https://doi.org/10.1111/nyas.13289openalex-snapshot

Antimicrobial resistance surveillance in the genomic age

inferredcites →https://doi.org/10.1126/science.1159483openalex-snapshot

Antibiotics and Antibiotic Resistance Genes in Natural Environments

inferredcites →https://doi.org/10.1128/aac.01121-16openalex-snapshot

Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device

inferredcites →https://doi.org/10.1128/aem.02340-17openalex-snapshot

Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples

inferredcites →https://doi.org/10.1128/jb.00152-08openalex-snapshot

The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance

inferredcites →https://doi.org/10.1128/mmbr.00056-13openalex-snapshot

Integrons: Past, Present, and Future

inferredcites →https://doi.org/10.1155/2016/2475067openalex-snapshot

Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens

inferredcites →https://doi.org/10.1186/s12864-015-2153-5openalex-snapshot

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

inferredcites →https://doi.org/10.1186/s13073-015-0220-9openalex-snapshot

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

inferredcites →https://doi.org/10.1186/s40168-017-0353-8openalex-snapshot

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

inferredcites →https://doi.org/10.1186/s40168-018-0401-zopenalex-snapshot

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

inferredcites →https://doi.org/10.1186/s40168-018-0516-2openalex-snapshot

Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection

inferredcites →https://doi.org/10.1186/s40545-017-0118-6openalex-snapshot

Antimicrobial resistance in India

inferredcites →https://doi.org/10.12688/f1000research.7201.1openalex-snapshot

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

inferredcites →https://doi.org/10.1371/journal.pone.0019984openalex-snapshot

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

inferredcites →https://doi.org/10.1371/journal.pone.0162442openalex-snapshot

MetaStorm: A Public Resource for Customizable Metagenomics Annotation

inferredcites →https://doi.org/10.1373/clinchem.2008.107565openalex-snapshot

Metagenomic Pyrosequencing and Microbial Identification

inferredcites →https://doi.org/10.2217/fmb.11.135openalex-snapshot

Insights into Antibiotic Resistance Through Metagenomic Approaches

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.jhazmat.2021.127407openalex-snapshot

Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle

inferred← citeshttps://doi.org/10.1016/j.mimet.2020.106123openalex-snapshot

Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies

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