MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences

Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant

(2020) Maria Pachetti et al.   Journal of Translational Medicine

SARS-CoV-2 (COVID-19) by the numbers

(2020) Yinon M Bar-On et al.   eLife

simuG: a general-purpose genome simulator

(2019) Jia-Xing Yue et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

(2017) Yuelong Shu et al.   Eurosurveillance

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century

(2014) Oumar Faye et al.   PLoS Neglected Tropical Diseases

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Coronaviruses

(2011) Mark R. Denison et al.   RNA Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna 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

Future prospects for the treatment of rapidly evolving viral pathogens: insights from evolutionary biology

(2008) Esteban Domingo et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS