Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms

Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing

(2019) Andre Mu et al.   mSphere

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification

(2019) Florian P Breitwieser et al.   BIOINFORMATICS

Clonal Emergence of Invasive Multidrug-Resistant Staphylococcus epidermidis Deconvoluted via a Combination of Whole-Genome Sequencing and Microbiome Analyses

(2018) Xiqi Li et al.   CLINICAL INFECTIOUS DISEASES

Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

(2018) Pranita D. Tamma et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples

(2018) Liana E. Kafetzopoulou et al.   Eurosurveillance

Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer

(2018) Daniel Golparian et al.   Scientific Reports

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates

(2017) Jamie K. Lemon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Evaluation of Multiple Methods for Detection of Gastrointestinal Colonization of Carbapenem-Resistant Organisms from Rectal Swabs

(2016) Patricia J. Simner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS