Evaluating the effect of reference genome divergence on the analysis of empirical RADseq datasets

Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout

(2019) Justin Bohling et al.   CONSERVATION GENETICS

Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

(2019) Vera M. Warmuth et al.   Molecular Ecology Resources

Genomic Characterization of Coho Salmon Spawning Populations from the Hood Canal

(2019) Justin Bohling et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Inferring phylogenetic structure, hybridization and divergence times within Salmoninae (Teleostei: Salmonidae) using RAD-sequencing

(2018) Laurène A. Lecaudey et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

(2018) Kris A. Christensen et al.   PLoS One

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

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

(2018) Úlfur Árnason et al.   Science Advances

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly

(2018) Kris A. Christensen et al.   PLoS One

Allele frequency-free inference of close familial relationships from genotypes or low depth sequencing data

(2018) Ryan K Waples et al.   MOLECULAR ECOLOGY

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering

(2017) Richard G. J. Hodel et al.   Scientific Reports

Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

(2016) Emily D. Fountain et al.   Molecular Ecology Resources

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Harnessing the power of RADseq for ecological and evolutionary genomics

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

Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions

(2016) Emily E. Puckett   Conservation Genetics Resources

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

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

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

(2016) B. M. vonHoldt et al.   Science Advances

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

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

(2014) B. Nevado et al.   MOLECULAR ECOLOGY

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: Analysis of mtDNA data

(2013) S. V. Shedko et al.   RUSSIAN JOURNAL OF GENETICS

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

The tiger genome and comparative analysis with lion and snow leopard genomes

(2013) Yun Sung Cho et al.   Nature Communications

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Framing the Salmonidae Family Phylogenetic Portrait: A More Complete Picture from Increased Taxon Sampling

(2012) Alexis Crête-Lafrenière et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River

(2011) NATHAN R. CAMPBELL et al.   Molecular Ecology Resources

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Genetic Structure, Evolutionary History, and Conservation Units of Bull Trout in the Coterminous United States

(2011) William R. Ardren et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY