Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

Clinical and biological insights from viral genome sequencing

(2017) Charlotte J. Houldcroft et al.   NATURE REVIEWS MICROBIOLOGY

Harmonization of nucleic acid testing for Zika virus: development of the 1st World Health Organization International Standard

(2017) Sally A. Baylis et al.   TRANSFUSION

Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes

(2016) Emma Thomson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method

(2016) Julianne R. Brown et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Outbreak of Zika Virus Infection, Chiapas State, Mexico, 2015, and First Confirmed Transmission byAedes aegyptiMosquitoes in the Americas

(2016) Mathilde Guerbois et al.   JOURNAL OF INFECTIOUS DISEASES

1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

(2016) Michael Worobey et al.   NATURE

The evolution of Ebola virus: Insights from the 2013–2016 epidemic

(2016) Edward C. Holmes et al.   NATURE

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Isolation of a Novel Insect-Specific Flavivirus fromCuliseta melanurain the Northeastern United States

(2016) Michael J. Misencik et al.   VECTOR-BORNE AND ZOONOTIC DISEASES

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

(2015) Kristian G. Andersen et al.   CELL

SureSelect target enrichment: A robust and sensitive method for sequencing of whole norovirus genomes direct from clinical specimens

(2015) J.R. Brown et al.   JOURNAL OF CLINICAL VIROLOGY

Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa

(2015) Miles W. Carroll et al.   NATURE

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

(2015) Andy Kilianski et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples

(2013) Elizabeth M. Batty et al.   PLoS One

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster 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

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Skip the Alignment: Degenerate, Multiplex Primer and Probe Design Using K-mer Matching Instead of Alignments

(2012) David A. Hysom et al.   PLoS One

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

(2012) Kelvin Li et al.   Virology Journal

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes

(2010) Qing Yu et al.   BIOINFORMATICS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

(2009) Shota Nakamura et al.   PLoS One

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE