Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions

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

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

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics

(2019) Jose Manuel Martí   PLoS Computational Biology

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

(2019) Themoula Charalampous et al.   NATURE BIOTECHNOLOGY

FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses

(2018) Kathrin M Seibt et al.   BIOINFORMATICS

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

(2018) Raga Krishnakumar et al.   Scientific Reports

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Looking back at yellow fever in Angola

(2017) Sanjeet Bagcchi   LANCET INFECTIOUS DISEASES

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

(2017) Nathan D. Grubaugh et al.   NATURE

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Zika's emerging threat for the Asia-Pacific region

(2016) The Lancet   LANCET

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

The Zika Challenge

(2016) Charlotte J. Haug et al.   NEW ENGLAND JOURNAL OF MEDICINE

Assessing the global threat from Zika virus

(2016) J. Lessler et al.   SCIENCE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

A fatal yellow fever virus infection in China: description and lessons

(2016) Zhihai Chen et al.   Emerging Microbes & Infections

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

(2016) Yang Li et al.   Scientific Reports

Dissemination, divergence and establishment of H7N9 influenza viruses in China

(2015) Tommy Tsan-Yuk Lam et al.   NATURE

Spread of MERS to South Korea and China

(2015) David S Hui et al.   Lancet Respiratory Medicine

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome jigsaw

(2013) Vivien Marx   NATURE

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS