Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

(2016) N. Snyder-Mackler et al.   GENETICS

Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms

(2016) Cyrielle Gasc et al.   NUCLEIC ACIDS RESEARCH

Improving the estimation of genetic distances from Next-Generation Sequencing data

(2015) Filipe G. Vieira et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

SNP genotyping and population genomics from expressed sequences - current advances and future possibilities

(2015) Pierre De Wit et al.   MOLECULAR ECOLOGY

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Genome skimming for next-generation biodiversity analysis

(2015) Steven Dodsworth   TRENDS IN PLANT SCIENCE

Signatures of selection in tilapia revealed by whole genome resequencing

(2015) Jun Hong Xia et al.   Scientific Reports

Differential Nuclear and Mitochondrial DNA Preservation in Post-Mortem Teeth with Implications for Forensic and Ancient DNA Studies

(2015) Denice Higgins et al.   PLoS One

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

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

Reference-free SNP detection: dealing with the data deluge

(2014) Richard M Leggett et al.   BMC GENOMICS

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Genome-Wide Estimation of Linkage Disequilibrium from Population-Level High-Throughput Sequencing Data

(2014) Takahiro Maruki et al.   GENETICS

Trade-offs and utility of alternative RADseq methods: Reply to Puritzet al.

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

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

Unexpected ancestry ofPopulusseedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

(2014) Dorothea Lindtke et al.   MOLECULAR ECOLOGY

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

(2014) Zachariah Gompert et al.   MOLECULAR ECOLOGY

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Reference-free detection of isolated SNPs

(2014) Raluca Uricaru et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

Improved workflows for high throughput library preparation using the transposome-based nextera system

(2013) Sarah Lamble et al.   BMC BIOTECHNOLOGY

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

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

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

(2013) Iratxe Montes et al.   PLoS One

Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

(2013) Matteo Fumagalli   PLoS One

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

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

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

Spatial scale and divergent patterns of variation in adapted traits in the ocean

(2012) Lyndie A. Hice et al.   ECOLOGY LETTERS

Association Testing for Next-Generation Sequencing Data Using Score Statistics

(2012) Line Skotte et al.   GENETIC EPIDEMIOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

(2012) Pierre De Wit et al.   Molecular Ecology Resources

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

(2012) M. E. Allentoft et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais 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

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

Genome-wide polymorphisms show unexpected targets of natural selection

(2011) M. H. Pespeni et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential

(2010) Megan E. Mach et al.   MARINE BIOLOGY

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

(2009) D. H. E. Setiamarga et al.   Biology Letters

New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains

(2009) Carsten Schwarz et al.   NUCLEIC ACIDS RESEARCH

Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences

(2008) Davin H.E. Setiamarga et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS