From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

Too much of a good thing? Finding the most informative genetic dataset to answer conservation questions

(2019) Elspeth A. McLennan et al.   Molecular Ecology Resources

Genome sequencing and conservation genomics in the Scandinavian wolverine population

(2018) Robert Ekblom et al.   CONSERVATION BIOLOGY

First de novo whole genome sequencing and assembly of the pink-footed goose

(2018) J.M. Pujolar et al.   GENOMICS

Density trends and demographic signals uncover the long-term impact of transmissible cancer in Tasmanian devils

(2018) Billie T. Lazenby et al.   JOURNAL OF APPLIED ECOLOGY

Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species

(2018) F. Maroso et al.   Marine Genomics

dartr : An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing

(2018) Bernd Gruber et al.   Molecular Ecology Resources

Adaptation and conservation insights from the koala genome

(2018) Rebecca N. Johnson et al.   NATURE GENETICS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild

(2018) Catherine E. Grueber et al.   Evolutionary Applications

Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age

(2017) J. M. Pujolar et al.   MOLECULAR ECOLOGY

Deriving genotypes from RAD-seq short-read data using Stacks

(2017) Nicolas C Rochette et al.   Nature Protocols

Genotype Calling from Population-Genomic Sequencing Data

(2017) Takahiro Maruki et al.   G3-Genes Genomes Genetics

Bridging the conservation genetics gap by identifying barriers to implementation for conservation practitioners

(2017) Helen R. Taylor et al.   Global Ecology and Conservation

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

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

“Devil Tools & Tech”: A Synergy of Conservation Research and Management Practice

(2016) Carolyn J. Hogg et al.   Conservation Letters

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

(2016) Aaron B. A. Shafer et al.   Methods in Ecology and Evolution

Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies

(2016) Davoud Torkamaneh et al.   PLoS One

Influence of genetic provenance and birth origin on productivity of the Tasmanian devil insurance population

(2015) Carolyn J. Hogg et al.   CONSERVATION GENETICS

Bird sequencing project takes off

(2015) Guojie Zhang   NATURE

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomic insights into a contagious cancer in Tasmanian devils

(2015) Catherine E. Grueber et al.   TRENDS IN GENETICS

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

(2013) Joseph Lachance et al.   BIOESSAYS

Comparing a few SNP calling algorithms using low-coverage sequencing data

(2013) Xiaoqing Yu et al.   BMC BIOINFORMATICS

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

(2012) Elizabeth P. Murchison et al.   CELL

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

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart 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

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

(2011) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

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

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

(2008) Thibaut Jombart   BIOINFORMATICS

Heterozygosity-fitness correlations and their relevance to studies on inbreeding depression in threatened species

(2008) CATHERINE E GRUEBER et al.   MOLECULAR ECOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One