ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

Genetic Variants of SARS-CoV-2—What Do They Mean?

(2021) Adam S. Lauring et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

COVID-19 evolution during the pandemic – Implications of new SARS-CoV-2 variants on disease control and public health policies

(2021) Cock van Oosterhout et al.   Virulence

HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

(2021) Phuoc Thien Truong Nguyen et al.   BMC BIOINFORMATICS

A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern

(2021) Matheus Filgueira Bezerra et al.   INFECTION GENETICS AND EVOLUTION

Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7

(2021) Dominik Nörz et al.   JOURNAL OF CLINICAL VIROLOGY

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

(2021) Felipe Gomes Naveca et al.   NATURE MEDICINE

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing

(2021) Christian Brandt et al.   Frontiers in Genetics

Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool

(2021) Áine O’Toole et al.   Virus Evolution

The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein

(2021) Paola Cristina Resende et al.   Virus Evolution

Optimization and Clinical Validation of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification, a Fast, Highly Sensitive and Specific COVID-19 Molecular Diagnostic Tool That Is Robust to Detect SARS-CoV-2 Variants of Concern

(2021) Pedro A. Alves et al.   Frontiers in Microbiology

Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

(2020) Zijie Shen et al.   CLINICAL INFECTIOUS DISEASES

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

(2020) Gubio S. Campos et al.   JOURNAL OF VIROLOGICAL METHODS

Clinical and Laboratory Diagnosis of SARS-CoV-2, the Virus Causing COVID-19

(2020) Severino Jefferson Ribeiro da Silva et al.   ACS Infectious Diseases

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

(2020) Sureshnee Pillay et al.   Genes

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

(2020) Caroline Charre et al.   Virus Evolution

Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

(2020) Marcelo Henrique Santos Paiva et al.   Viruses-Basel

OUP accepted manuscript

(2018)   BIOINFORMATICS

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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