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

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness

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

Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

(2020) F. Xavier López-Labrador et al.   JOURNAL OF CLINICAL VIROLOGY

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

(2019) L. E. Kafetzopoulou et al.   SCIENCE

Choice of assembly software has a critical impact on virome characterisation

(2019) Thomas D. S. Sutton et al.   Microbiome

CAMISIM: simulating metagenomes and microbial communities

(2019) Adrian Fritz et al.   Microbiome

Clinical metagenomics

(2019) Charles Y. Chiu et al.   NATURE REVIEWS GENETICS

Considerations for Genomic Data Privacy and Security when Working in the Cloud

(2019) Alexis B. Carter   JOURNAL OF MOLECULAR DIAGNOSTICS

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

(2019) Steve Miller et al.   GENOME RESEARCH

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

(2019) Jose Manuel Martí   PLoS Computational Biology

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

FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

(2019) Heike Sichtig et al.   Nature Communications

Correction: Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

(2019) Jose Manuel Martí   PLoS Computational Biology

Benchmarking Metagenomics Tools for Taxonomic Classification

(2019) Simon H. Ye et al.   CELL

Rethinking the ethical principles of genomic medicine services

(2019) Stephanie B. Johnson et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

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

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

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

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

Comparison of normalization methods for the analysis of metagenomic gene abundance data

(2018) Mariana Buongermino Pereira et al.   BMC GENOMICS

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

(2018) Valeria D’Argenio   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

(2018) Sam Nooij et al.   Frontiers in Microbiology

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

(2018) Norman Goodacre et al.   mSphere

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

(2018) Michael Vilsker et al.   BIOINFORMATICS

Clinically relevant thresholds for ultrasensitive HIV drug resistance testing: a multi-country nested case-control study

(2018) Seth C Inzaule et al.   Lancet HIV

GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets

(2018) Matthew D Czajkowski et al.   BIOINFORMATICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

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

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)

(2017) Elliot J Lefkowitz et al.   NUCLEIC ACIDS RESEARCH

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

A Quick Introduction to Version Control with Git and GitHub

(2016) John D. Blischak et al.   PLoS Computational Biology

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

Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data

(2015) Peipei Li et al.   BMC BIOINFORMATICS

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

(2015) Matthias Scheuch et al.   BMC BIOINFORMATICS

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

Astrovirus VA1/HMO-C: An Increasingly Recognized Neurotropic Pathogen in Immunocompromised Patients

(2015) Julianne R. Brown et al.   CLINICAL INFECTIOUS DISEASES

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

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

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

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic

(2015) Richard J. Hall et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

(2014) S. N. Naccache et al.   GENOME RESEARCH

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Quality control of next-generation sequencing data without a reference

(2014) Urmi H. Trivedi et al.   Frontiers in Genetics

Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community

(2012) Brett Pickett et al.   Viruses-Basel

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

(2011) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

(2009) D. S. Horner et al.   BRIEFINGS IN BIOINFORMATICS

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS