Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

(2021) Jutte J.C. de Vries et al.   JOURNAL OF CLINICAL VIROLOGY

Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics

(2020) Ellen C. Carbo et al.   JOURNAL OF CLINICAL VIROLOGY

STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies

(2020) Tehmina Bharucha et al.   LANCET INFECTIOUS DISEASES

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

(2019) Steve Miller et al.   GENOME RESEARCH

TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

(2019) Jiao Chen et al.   BMC BIOINFORMATICS

Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets

(2019) Annika Brinkmann et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

(2019) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial

(2019) Junier et al.   Genes

Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases

(2019) Kufner et al.   Genes

Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers

(2019) Hanna Jerome et al.   JOURNAL OF INFECTION

The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

(2019) Anneloes L. van Rijn et al.   PLoS One

DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples

(2019) Malik Alawi et al.   Scientific Reports

Pathogen identification by shotgun metagenomics of patients with necrotizing soft‐tissue infections

(2019) C. Rodriguez et al.   BRITISH JOURNAL OF DERMATOLOGY

Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients

(2019) Sander van Boheemen et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases

(2018) Julianne R. Brown et al.   JOURNAL OF INFECTION

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

(2018) Sam Nooij et al.   Frontiers in Microbiology

Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data

(2018) Michael Vilsker et al.   BIOINFORMATICS

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

(2017) David Paez-Espino et al.   Nature Protocols

Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection

(2017) Dagmara W. Lewandowska et al.   PLoS One

Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis

(2016) Sofia Morfopoulou et al.   ACTA NEUROPATHOLOGICA

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing

(2016) Jun-ichi Kawada et al.   Scientific Reports

VIP: an integrated pipeline for metagenomics of virus identification and discovery

(2016) Yang Li et al.   Scientific Reports

Bayesian mixture analysis for metagenomic community profiling

(2015) Sofia Morfopoulou et al.   BIOINFORMATICS

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

(2015) Matthias Scheuch et al.   BMC BIOINFORMATICS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Performance of Different Mono- and Multiplex Nucleic Acid Amplification Tests on a Multipathogen External Quality Assessment Panel

(2011) K. Loens et al.   JOURNAL OF CLINICAL MICROBIOLOGY

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH