Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)

(2019) Travis C. Glenn et al.   PeerJ

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

(2019) Natalia J. Bayona-Vásquez et al.   PeerJ

Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing

(2018) Laura E. MacConaill et al.   BMC GENOMICS

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

(2018) Maura Costello et al.   BMC GENOMICS

Computational correction of index switching in multiplexed sequencing libraries

(2018) Anton J M Larsson et al.   NATURE METHODS

Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources

(2018) Troy J. Kieran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

(2016) Richard C. Harrington et al.   BMC EVOLUTIONARY BIOLOGY

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

(2016) Sandra L. Hoffberg et al.   Molecular Ecology Resources

Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga

(2016) Bonnie B. Blaimer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

(2016) Matthew D. McGee et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq)

(2015) Carly F. Graham et al.   Molecular Ecology Resources

The complete mitochondrial DNA of endemic Eastern Pacific coral (Porites panamensis)

(2014) Miguel A. Del Río-Portilla et al.   Mitochondrial DNA

The complete mitochondrial DNA of the silky shark (Carcharhinus falciformis)

(2014) Carolina Galván-Tirado et al.   Mitochondrial DNA

The complete mitochondrial DNA of white shark (Carcharodon carcharias) from Isla Guadalupe, Mexico

(2014) Pindaro Diaz-Jaimes et al.   Mitochondrial DNA

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake

(2012) Todd A. Castoe et al.   PLoS One

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

Next Generation Molecular Ecology

(2010) DIETHARD TAUTZ et al.   MOLECULAR ECOLOGY

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

(2010) Andrew Adey et al.   GENOME BIOLOGY

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Identification of genetic variants using bar-coded multiplexed sequencing

(2008) David W Craig et al.   NATURE METHODS

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources