Sierra SARS-CoV-2 sequence and antiviral resistance analysis program

Structures of the Omicron Spike trimer with ACE2 and an anti-Omicron antibody

(2022) Wanchao Yin et al.   SCIENCE

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

(2022) Filipe Zimmer Dezordi et al.   Viruses-Basel

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

(2022) Chien-Chi Lo et al.   BIOINFORMATICS

COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data

(2022) Jody Phelan et al.   BMC BIOINFORMATICS

Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification

(2022) Priscilla S.-W. Yeung et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

(2022) Darren P. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons

(2022) Philip L. Tzou et al.   PLoS One

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

(2022) Matthew McCallum et al.   SCIENCE

De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report

(2022) Shiv Gandhi et al.   Nature Communications

PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification

(2022) Renato R. M. Oliveira et al.   PeerJ

In Vitro Selection of Remdesivir-Resistant SARS-CoV-2 Demonstrates High Barrier to Resistance

(2022) Liva Checkmahomed et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites

(2022) Sho Iketani et al.   Cell Host & Microbe

Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir

(2022) Kai S. Yang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance

(2022) Ala M. Shaqra et al.   Nature Communications

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

(2021) Tyler N. Starr et al.   SCIENCE

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

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

(2021) Darren P. Martin et al.   CELL

COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance

(2021) Michele Simonetti et al.   Nature Communications

In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2

(2021) Agnieszka M. Szemiel et al.   PLoS Pathogens

Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences

(2020) Philip L. Tzou et al.   PLoS One

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

Remdesivir failure with SARS-CoV-2 RNA-dependent RNA-polymerase mutation in a B-cell immunodeficient patient with protracted Covid-19

(2020) Martin Martinot et al.   CLINICAL INFECTIOUS DISEASES

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

(2020) Caroline Charre et al.   Virus Evolution

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease

(2018) Maria L. Agostini et al.   mBio

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

(2017) Yuelong Shu et al.   Eurosurveillance

Collaborative update of a rule-based expert system for HIV-1 genotypic resistance test interpretation

(2017) Roger Paredes et al.   PLoS One

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS