vcfr: a package to manipulate and visualize variant call format data in R

Population Genomics of Fungal and Oomycete Pathogens

(2016) Niklaus J. Grünwald et al.   Annual Review of Phytopathology

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

(2015) Zhian N. Kamvar et al.   Frontiers in Genetics

Rcpp: SeamlessRandC++Integration

(2015) Dirk Eddelbuettel et al.   Journal of Statistical Software

Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing

(2014) Nathan R. Campbell et al.   Molecular Ecology Resources

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

(2013) Michael D. Martin et al.   Nature Communications

Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

(2013) Fei Lu et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen

(2012) David E. L. Cooke et al.   PLoS Pathogens

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

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

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS