Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

(2022) Sarah Temmam et al.   NATURE

Detection of Phenuiviridae, Chuviridae Members, and a Novel Quaranjavirus in Hard Ticks From Danube Delta

(2022) Bianca Elena Bratuleanu et al.   Frontiers in Veterinary Science

Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results

(2021) Béatrice Regnault et al.   Viruses-Basel

First case of lethal encephalitis in Western Europe due to European bat lyssavirus type 1

(2021) Béatrice Regnault et al.   CLINICAL INFECTIOUS DISEASES

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

The virome of Rhipicephalus , Dermacentor and Haemaphysalis ticks from Eastern Romania includes novel viruses with potential relevance for public health

(2021) Bianca Elena Bratuleanu et al.   Transboundary and Emerging Diseases

RNA Viruses of Amblyomma variegatum and Rhipicephalus microplus and Cattle Susceptibility in the French Antilles

(2020) Mathilde Gondard et al.   Viruses-Basel

Report of the second international conference on next generation sequencing for adventitious virus detection in biologics for humans and animals

(2020) Arifa S. Khan et al.   BIOLOGICALS

Identification of Umbre Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 French Patients with Hypogammaglobulinemia

(2020) Philippe Pérot et al.   CLINICAL INFECTIOUS DISEASES

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

(2020) Katrina L Kalantar et al.   GigaScience

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

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

(2019) Maria Asplund et al.   CLINICAL MICROBIOLOGY AND INFECTION

Expanding the RNA Virosphere by Unbiased Metagenomics

(2019) Yong-Zhen Zhang et al.   Annual Review of Virology

Monitoring Silent Spillovers Before Emergence: A Pilot Study at the Tick/Human Interface in Thailand

(2019) Sarah Temmam et al.   Frontiers in Microbiology

Insights into the Host Range, Genetic Diversity, and Geographical Distribution of Jingmenviruses

(2019) Sarah Temmam et al.   mSphere

Whole genome sequencing and phylogenetic characterization of a novel bat-associated picornavirus-like virus with an unusual genome organization

(2019) Sarah Temmam et al.   INFECTION GENETICS AND EVOLUTION

GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts

(2018) Mark A Walker et al.   BIOINFORMATICS

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

(2018) Norman Goodacre et al.   mSphere

Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection

(2018) Christophe Lambert et al.   Viruses-Basel

Current Perspectives on High-Throughput Sequencing (HTS) for Adventitious Virus Detection: Upstream Sample Processing and Library Preparation

(2018) Siemon Ng et al.   Viruses-Basel

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

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

AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

(2013) Alexis Criscuolo et al.   GENOMICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY