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

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data

(2021) Susana Posada-Céspedes et al.   BIOINFORMATICS

A comprehensive profile of genomic variations in the SARS-CoV-2 isolates from the state of Telangana, India

(2021) Asmita Gupta et al.   JOURNAL OF GENERAL VIROLOGY

iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification

(2021) Sara Castellano et al.   Genes

Testing at scale during the COVID-19 pandemic

(2021) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants

(2021) João H. C. Campos et al.   Viruses-Basel

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

Cryptic transmission of SARS-CoV-2 in Washington state

(2020) Trevor Bedford et al.   SCIENCE

Comprehensive annotations of the mutational spectra of SARS‐CoV‐2 spike protein: a fast and accurate pipeline

(2020) Mohammad Shaminur Rahman et al.   Transboundary and Emerging Diseases

A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture

(2020) Jalees A. Nasir et al.   Viruses-Basel

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

(2017) Yuelong Shu et al.   Eurosurveillance

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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