A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples

Fast-spreading U.K. virus variant raises alarms

(2021) Kai Kupferschmidt   SCIENCE

Delta variant triggers new phase in the pandemic

(2021) Kai Kupferschmidt et al.   SCIENCE

Comparison of different samples for 2019 novel coronavirus detection by nucleic acid amplification tests

(2020) Chunbao Xie et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

(2020) Jasper Fuk-Woo Chan et al.   LANCET

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Clinical Characteristics of Coronavirus Disease 2019 in China

(2020) Wei-jie Guan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany

(2020) Camilla Rothe et al.   NEW ENGLAND JOURNAL OF MEDICINE

Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases

(2020) Tao Ai et al.   RADIOLOGY

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

(2020) Yong-Zhen Zhang et al.   CELL

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

(2020) Jing Lu et al.   CELL

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

(2020) D. Paraskevis et al.   INFECTION GENETICS AND EVOLUTION

Viral and host factors related to the clinical outcome of COVID-19

(2020) Xiaonan Zhang et al.   NATURE

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

The COVID-19 vaccine development landscape

(2020) Tung Thanh Le et al.   NATURE REVIEWS DRUG DISCOVERY

Phylogenetic network analysis of SARS-CoV-2 genomes

(2020) Peter Forster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

(2020) Minfeng Xiao et al.   Genome Medicine

Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100TM System

(2020) Véronique Hourdel et al.   Frontiers in Microbiology

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA)

(2017) Mette Myrmel et al.   PLoS One

Examining Sources of Error in PCR by Single-Molecule Sequencing

(2017) Vladimir Potapov et al.   PLoS One

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

(2016) Philip Ewels et al.   BIOINFORMATICS

The impact of amplification on differential expression analyses by RNA-seq

(2016) Swati Parekh et al.   Scientific Reports

The Impact of DNA Input Amount and DNA Source on the Performance of Whole-Exome Sequencing in Cancer Epidemiology

(2015) Q. Zhu et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Comparison of somatic mutation calling methods in amplicon and whole exome sequence data

(2014) Huilei Xu et al.   BMC GENOMICS

Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

(2013) Sachin Sah et al.   Genome Medicine

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS