Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples
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Title
Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples
Authors
Keywords
-
Journal
Frontiers in Cellular and Infection Microbiology
Volume 8, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2018-10-23
DOI
10.3389/fcimb.2018.00375
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- (2018) CLINICAL INFECTIOUS DISEASES
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- (2017) Artur J. Sabat et al. Scientific Reports
- Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
- (2017) Anjuli Meiser et al. Scientific Reports
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- (2017) Dagmara W. Lewandowska et al. PLoS One
- Centrifuge: rapid and sensitive classification of metagenomic sequences
- (2016) Daehwan Kim et al. GENOME RESEARCH
- Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing
- (2016) Mohammad R. Hasan et al. JOURNAL OF CLINICAL MICROBIOLOGY
- High-throughput sequencing of cerebrospinal fluid for diagnosis of chronicPropionibacterium acnesmeningitis in an allogeneic stem cell transplant recipient
- (2016) K.M. Wylie et al. Transplant Infectious Disease
- Fast and sensitive taxonomic classification for metagenomics with Kaiju
- (2016) Peter Menzel et al. Nature Communications
- Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing
- (2016) Jun-ichi Kawada et al. Scientific Reports
- An evaluation of the accuracy and speed of metagenome analysis tools
- (2016) Stinus Lindgreen et al. Scientific Reports
- Fatal Psychrobacter sp. infection in a pediatric patient with meningitis identified by metagenomic next-generation sequencing in cerebrospinal fluid
- (2015) Ortiz-Alcántara Joanna María et al. ARCHIVES OF MICROBIOLOGY
- Delftia Acidovorans: A Rare Pathogen in Immunocompetent and Immunocompromised Patients
- (2015) Huseyin Bilgin et al. Canadian Journal of Infectious Diseases & Medical Microbiology
- Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses
- (2015) S. Cordey et al. CLINICAL MICROBIOLOGY AND INFECTION
- Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains
- (2015) Dagmara W. Lewandowska et al. DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
- Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens
- (2015) Karol Perlejewski et al. JOURNAL OF VIROLOGICAL METHODS
- Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
- (2015) Alexander L. Greninger et al. Genome Medicine
- Target-Dependent Enrichment of Virions Determines the Reduction of High-Throughput Sequencing in Virus Discovery
- (2015) Randi Holm Jensen et al. PLoS One
- RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data
- (2015) Simon H. Tausch et al. PLoS One
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- Rothia Bacteremia: a 10-Year Experience at Mayo Clinic, Rochester, Minnesota
- (2014) Poornima Ramanan et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes
- (2014) Martin Laurence et al. PLoS One
- Encephalitis Hospitalization Rates and Inpatient Mortality in the United States, 2000-2010
- (2014) Benjamin P. George et al. PLoS One
- Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data
- (2014) Richard W. Lusk PLoS One
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery
- (2013) Richard J. Hall et al. JOURNAL OF VIROLOGICAL METHODS
- The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns
- (2013) S. N. Naccache et al. JOURNAL OF VIROLOGY
- Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer
- (2013) Saskia L. Smits et al. PLoS One
- Identification of a New Cyclovirus in Cerebrospinal Fluid of Patients with Acute Central Nervous System Infections
- (2013) L. V. Tan et al. mBio
- CD-HIT: accelerated for clustering the next-generation sequencing data
- (2012) Limin Fu et al. BIOINFORMATICS
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
- (2012) Y. Peng et al. BIOINFORMATICS
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Enteroviral Meningitis Does Not Exclude Concurrent Bacterial Meningitis
- (2011) Romain Basmaci et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Evaluation of High-Throughput Sequencing for Identifying Known and Unknown Viruses in Biological Samples
- (2011) Justine Cheval et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Raw Sewage Harbors Diverse Viral Populations
- (2011) P. G. Cantalupo et al. mBio
- Acute encephalitis
- (2010) B. Sivertsen et al. ACTA NEUROLOGICA SCANDINAVICA
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- Septic arthritis due to Rothia mucilaginosa
- (2010) A. J. Kaasch et al. INFECTION
- Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study
- (2010) Julia Granerod et al. LANCET INFECTIOUS DISEASES
- Infectious Encephalitis in France in 2007: A National Prospective Study
- (2009) Alexandra Mailles et al. CLINICAL INFECTIOUS DISEASES
- Comamonas TestosteroniMeningitis in a Homeless Man
- (2008) Long Jin et al. JOURNAL OF FORENSIC SCIENCES
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- (2008) T. F. F. Ng et al. JOURNAL OF VIROLOGY
- A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases
- (2008) Gustavo Palacios et al. NEW ENGLAND JOURNAL OF MEDICINE
- Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
- (2008) H. Feng et al. SCIENCE
- Rapid Identification of Known and New RNA Viruses from Animal Tissues
- (2008) Joseph G. Victoria et al. PLoS Pathogens
- Bacterial meningitis fromRothia mucilaginosain patients with malignancy or undergoing hematopoietic stem cell transplantation
- (2007) Alisa B. Lee et al. PEDIATRIC BLOOD & CANCER
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