RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies

(2020) Shibo Jiang et al.   Emerging Microbes & Infections

Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan

(2020) Jasper Fuk-Woo Chan et al.   Emerging Microbes & Infections

Meta-transcriptomics and the evolutionary biology of RNA viruses

(2018) Mang Shi et al.   VIRUS RESEARCH

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

(2018) Wei Gu et al.   Annual Review of Pathology-Mechanisms of Disease

Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus

(2017) Ben Hu et al.   PLoS Pathogens

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

(2015) Dinghua Li et al.   BIOINFORMATICS

A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence

(2015) Vineet D Menachery et al.   NATURE MEDICINE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY