A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
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Title
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
Authors
Keywords
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Journal
Frontiers in Genetics
Volume 10, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2020-02-21
DOI
10.3389/fgene.2019.01407
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Note: Only part of the references are listed.- Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes
- (2019) Thomas L. P. Couvreur et al. Frontiers in Plant Science
- Long‐fragment targeted capture for long‐read sequencing of plastomes
- (2019) Kevin Bethune et al. Applications in Plant Sciences
- Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods
- (2019) Andrea Lienhard et al. PeerJ
- Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies
- (2019) Pável Matos-Maraví et al. PeerJ
- Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae
- (2019) Oriane Loiseau et al. Frontiers in Plant Science
- Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms
- (2019) Grace E. Brewer et al. Frontiers in Plant Science
- Hyb-Seq for Flowering Plant Systematics
- (2019) Steven Dodsworth et al. TRENDS IN PLANT SCIENCE
- Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)
- (2019) Travis C. Glenn et al. PeerJ
- The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques
- (2019) Laura L. Forrest et al. Frontiers in Ecology and Evolution
- MrBait: universal identification and design of targeted-enrichment capture probes
- (2018) Tyler K Chafin et al. BIOINFORMATICS
- Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms
- (2018) Maura Costello et al. BMC GENOMICS
- A Comprehensive and Dated Phylogenomic Analysis of Butterflies
- (2018) Marianne Espeland et al. CURRENT BIOLOGY
- Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set
- (2018) Akito Y. Kawahara et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements
- (2018) Tobias Andermann et al. SYSTEMATIC BIOLOGY
- Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
- (2018) Saman Saeidi et al. Jove-Journal of Visualized Experiments
- SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
- (2018) Tobias Andermann et al. PeerJ
- Hybridization capture reveals microbial diversity missed using current profiling methods
- (2018) Cyrielle Gasc et al. Microbiome
- Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary
- (2018) Michael E. Alfaro et al. Nature Ecology & Evolution
- A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms
- (2018) Marylaure de La Harpe et al. Molecular Ecology Resources
- Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes
- (2018) Gaetan J. A. Thilliez et al. NEW PHYTOLOGIST
- A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering
- (2018) Matthew G Johnson et al. SYSTEMATIC BIOLOGY
- Targeted capture of complete coding regions across divergent species
- (2017) Ryan K Schott et al. Genome Biology and Evolution
- Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa
- (2017) Ramprasad Neethiraj et al. MOLECULAR ECOLOGY
- Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems
- (2017) Andrea M. Quattrini et al. Molecular Ecology Resources
- Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles
- (2017) Sonal Singhal et al. Molecular Ecology Resources
- Reconstructing the genome of the most recent common ancestor of flowering plants
- (2017) Florent Murat et al. NATURE GENETICS
- High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
- (2017) Julien Lagarde et al. NATURE GENETICS
- A new model for ancient DNA decay based on paleogenomic meta-analysis
- (2017) Logan Kistler et al. NUCLEIC ACIDS RESEARCH
- The factors affecting the reproducibility of micro-volume DNA mass quantification in Nanodrop 2000 spectrophotometer
- (2017) Songcheng Yu et al. OPTIK
- Phylogenomics from Whole Genome Sequences Using aTRAM
- (2017) Julie M. Allen et al. SYSTEMATIC BIOLOGY
- Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing
- (2017) Noelle R. Noyes et al. Microbiome
- Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
- (2016) Heng Li BIOINFORMATICS
- A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing
- (2016) Tian-Hao Zhang et al. BMC GENOMICS
- The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
- (2016) James E. Tarver et al. Genome Biology and Evolution
- BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design
- (2016) Christoph Mayer et al. MOLECULAR BIOLOGY AND EVOLUTION
- Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms
- (2016) Hao Yuan et al. Molecular Ecology Resources
- Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture
- (2016) Luisa C. Teasdale et al. Molecular Ecology Resources
- Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes
- (2016) Fátima Sánchez Barreiro et al. Molecular Ecology Resources
- A comparison of DNA extraction methods for high-throughput DNA analyses
- (2016) Lauren M. Schiebelhut et al. Molecular Ecology Resources
- Experimental conditions improving in-solution target enrichment for ancient DNA
- (2016) Diana I. Cruz-Dávalos et al. Molecular Ecology Resources
- RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data
- (2016) Sandra L. Hoffberg et al. Molecular Ecology Resources
- An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
- (2016) Daniel M. Portik et al. Molecular Ecology Resources
- Exon capture optimization in amphibians with large genomes
- (2016) Evan McCartney-Melstad et al. Molecular Ecology Resources
- Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
- (2016) Carl J. Rothfels et al. NEW PHYTOLOGIST
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms
- (2016) Cyrielle Gasc et al. NUCLEIC ACIDS RESEARCH
- Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics
- (2016) Michael G. Harvey et al. SYSTEMATIC BIOLOGY
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- (2016) Michelle L. Hart et al. TAXON
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- (2016) Matthew G. Johnson et al. Applications in Plant Sciences
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- (2016) Laura A. Hug et al. Nature Microbiology
- Capturing protein-coding genes across highly divergent species
- (2016) Chenhong Li et al. BIOTECHNIQUES
- Library construction for next-generation sequencing: Overviews and challenges
- (2016) Steven R. Head et al. BIOTECHNIQUES
- Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens
- (2016) Tomasz Suchan et al. PLoS One
- Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens
- (2016) Bonnie B. Blaimer et al. PLoS One
- Comparison of DNA Quantification Methods for Next Generation Sequencing
- (2016) Jérôme D. Robin et al. Scientific Reports
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- (2016) Santosh Anand et al. Scientific Reports
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- Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture
- (2015) Karolina Heyduk et al. BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
- MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
- (2015) Sandeep K Kushwaha et al. BMC BIOINFORMATICS
- PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations
- (2015) Min Wang et al. BMC GENOMICS
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- (2015) Todd N. Wylie et al. GENOME RESEARCH
- The use of museum specimens with high-throughput DNA sequencers
- (2015) Andrew S. Burrell et al. JOURNAL OF HUMAN EVOLUTION
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- (2015) Matthew R. Jones et al. MOLECULAR ECOLOGY
- Impact of enrichment conditions on cross-species capture of fresh and degraded DNA
- (2015) Johanna L. A. Paijmans et al. Molecular Ecology Resources
- Sequence capture of ultraconserved elements from bird museum specimens
- (2015) John E. McCormack et al. Molecular Ecology Resources
- Exon capture phylogenomics: efficacy across scales of divergence
- (2015) Jason G. Bragg et al. Molecular Ecology Resources
- Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing
- (2015) Cristina Gamba et al. Molecular Ecology Resources
- A complete bacterial genome assembled de novo using only nanopore sequencing data
- (2015) Nicholas J Loman et al. NATURE METHODS
- Capturing prokaryotic dark matter genomes
- (2015) Cyrielle Gasc et al. RESEARCH IN MICROBIOLOGY
- MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes
- (2015) Srikar Chamala et al. Applications in Plant Sciences
- A Protocol for Targeted Enrichment of Intron-Containing Sequence Markers for Recent Radiations: A Phylogenomic Example from Heuchera (Saxifragaceae)
- (2015) Ryan A. Folk et al. Applications in Plant Sciences
- 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
- The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus
- (2014) Martin J Thompson et al. BMC EVOLUTIONARY BIOLOGY
- A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics
- (2014) Katriina L. Ilves et al. Molecular Ecology Resources
- Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
- (2014) Brant C. Faircloth et al. Molecular Ecology Resources
- Sequencing pools of individuals — mining genome-wide polymorphism data without big funding
- (2014) Christian Schlötterer et al. NATURE REVIEWS GENETICS
- Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species
- (2014) Adam Healey et al. Plant Methods
- Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing
- (2014) Filipe de Sousa et al. PLoS One
- Ten years of next-generation sequencing technology
- (2014) Erwin L. van Dijk et al. TRENDS IN GENETICS
- A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)
- (2013) Brant C. Faircloth et al. PLoS One
- Targeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time
- (2013) Shannon M. Hedtke et al. PLoS One
- Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes
- (2013) Andaine Seguin-Orlando et al. PLoS One
- Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments
- (2013) J. Dabney et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae)
- (2013) YARELI ESQUER GARRIGOS et al. ZOOTAXA
- Targeted sequence capture as a powerful tool for evolutionary analysis1
- (2012) Corrinne E. Grover et al. AMERICAN JOURNAL OF BOTANY
- KASpOD—a web service for highly specific and explorative oligonucleotide design
- (2012) Nicolas Parisot et al. BIOINFORMATICS
- Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales
- (2012) Ke Bi et al. BMC GENOMICS
- Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
- (2012) N. Rohland et al. GENOME RESEARCH
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
- (2012) David Bryant et al. MOLECULAR BIOLOGY AND EVOLUTION
- Inferring Phylogenies from RAD Sequence Data
- (2012) Benjamin E. R. Rubin et al. PLoS One
- A High-Coverage Genome Sequence from an Archaic Denisovan Individual
- (2012) M. Meyer et al. SCIENCE
- Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
- (2012) Alan R. Lemmon et al. SYSTEMATIC BIOLOGY
- Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
- (2012) Brant C. Faircloth et al. SYSTEMATIC BIOLOGY
- HiSpOD: probe design for functional DNA microarrays
- (2011) Eric Dugat-Bony et al. BIOINFORMATICS
- The GENCODE exome: sequencing the complete human exome
- (2011) Alison J Coffey et al. EUROPEAN JOURNAL OF HUMAN GENETICS
- Chelex without boiling, a rapid and easy technique to obtain stable amplifiable DNA from small amounts of ethanol-stored spiders
- (2011) JULIANE CASQUET et al. Molecular Ecology Resources
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
- (2011) Manfred G Grabherr et al. NATURE BIOTECHNOLOGY
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing
- (2011) John W. Davey et al. NATURE REVIEWS GENETICS
- Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
- (2011) Martin Kircher et al. NUCLEIC ACIDS RESEARCH
- A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
- (2011) Robert J. Elshire et al. PLoS One
- Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
- (2011) Daniel Aird et al. GENOME BIOLOGY
- Optimal algorithms for haplotype assembly from whole-genome sequence data
- (2010) D. He et al. BIOINFORMATICS
- Fast and accurate long-read alignment with Burrows–Wheeler transform
- (2010) Heng Li et al. BIOINFORMATICS
- Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development
- (2010) Sébastien Terrat et al. BMC BIOINFORMATICS
- Genomic-scale capture and sequencing of endogenous DNA from feces
- (2010) GEORGE H. PERRY et al. MOLECULAR ECOLOGY
- Target-enrichment strategies for next-generation sequencing
- (2010) Lira Mamanova et al. NATURE METHODS
- The European Nucleotide Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- The Sequence Read Archive
- (2010) R. Leinonen et al. NUCLEIC ACIDS RESEARCH
- A Draft Sequence of the Neandertal Genome
- (2010) R. E. Green et al. SCIENCE
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- ABySS: A parallel assembler for short read sequence data
- (2009) J. T. Simpson et al. GENOME RESEARCH
- A rapid column-based ancient DNA extraction method for increased sample throughput
- (2009) NADIN ROHLAND et al. Molecular Ecology Resources
- Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
- (2009) Andreas Gnirke et al. NATURE BIOTECHNOLOGY
- Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
- (2009) Adrian W. Briggs et al. NUCLEIC ACIDS RESEARCH
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- (2008) D. R. Zerbino et al. GENOME RESEARCH
- Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
- (2008) Nathan A. Baird et al. PLoS One
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