Reference health
Estimating and accounting for genotyping errors in RAD‐seq experiments
57/57 checkable references clean · checked 2026-07-22
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
4 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 57 checked references that resolve
resolves10.1111/mec.12276
<scp>RAD</scp>seq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
resolves10.1371/journal.pone.0003376
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
resolves10.1111/mec.12105
Population genomics based on low coverage sequencing: how low should we go?
resolves10.1002/ece3.512
Is <scp>RAD</scp>‐seq suitable for phylogenetic inference? An in silico assessment and optimization
resolves10.1093/nar/gkr217
A method for counting PCR template molecules with application to next-generation sequencing
resolves10.1186/1471-2164-15-1104
Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo
resolves10.1111/mec.13587
Selection against recombinant hybrids maintains reproductive isolation in hybridizing <i>Populus</i> species despite F<sub>1</sub> fertility and recurrent gene flow
resolves10.1111/mec.13765
Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow
resolves10.1186/1471-2164-12-4
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley
resolves10.1371/journal.pgen.1005631
GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data
resolves10.1111/mec.12084
Special features of<scp>RAD</scp>Sequencing data: implications for genotyping
resolves10.1038/ng.806
A framework for variation discovery and genotyping using next-generation DNA sequencing data
resolves10.1073/pnas.1006538107
Resolving postglacial phylogeography using high-throughput sequencing
resolves10.1111/1755-0998.13087
Attack of the PCR clones: Rates of clonality have little effect on RAD‐seq genotype calls
resolves10.1093/bioinformatics/btu041
<i>ngsTools</i>: methods for population genetics analyses from next-generation sequencing data
resolves10.1111/mec.12089
The effect of<scp>RAD</scp>allele dropout on the estimation of genetic variation within and between populations
resolves10.1111/mec.12811
Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants
resolves10.1073/pnas.1318945111
High-throughput sequencing reveals inbreeding depression in a natural population
resolves10.1093/bioinformatics/btx474
fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample
resolves10.1371/journal.pone.0147209
Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding
resolves10.1093/gbe/evv026
Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
resolves10.1111/j.1365-294X.2012.05744.x
Recombinant hybrids retain heterozygosity at many loci: new insights into the genomics of reproductive isolation in<i><scp>P</scp>opulus</i>
resolves10.1111/mec.12759
Unexpected ancestry of <i>Populus</i> seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species
resolves10.1101/gr.119792.110
A reduced representation approach to population genetic analyses and applications to human evolution
resolves10.1038/hdy.2011.35
Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species
resolves10.1371/journal.pgen.1005887
Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback
resolves10.1111/1755-0998.12291
Restriction site‐associated <scp>DNA</scp> sequencing, genotyping error estimation and <i>de novo</i> assembly optimization for population genetic inference
resolves10.1101/gr.5681207
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
resolves10.1101/gr.169292.113
Population genomics of parallel hybrid zones in the mimetic butterflies,
<i>H. melpomene</i>
and
<i>H. erato</i>
resolves10.1371/journal.pone.0037135
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
resolves10.1007/s11032-016-0572-x
Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Elaeis guineensis)
resolves10.1371/journal.pone.0097589
fcGENE: A Versatile Tool for Processing and Transforming SNP Datasets
resolves10.1186/s12864-017-3767-6
Extremely low-coverage whole genome sequencing in South Asians captures population genomics information
resolves10.1086/502802
A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
resolves10.1086/BBLv227n2p146
Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters
resolves10.1111/mec.12011
Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species
resolves10.1126/science.1128691
The Genome of Black Cottonwood,
<i>Populus trichocarpa</i>
(Torr. & Gray)
resolves10.1101/gr.168393.113
Estimating genotype error rates from high-coverage next-generation sequence data
resolves10.1038/ng.894
Recombination rates in admixed individuals identified by ancestry-based inference
The 4 references without a DOI — listed, not checked
no DOI — not checkedFastQC: A quality control tool for high throughput sequence data
no DOI — not checkedea‐utils: Command‐line tools for processing biological sequencing data
no DOI — not checkedAligning sequence reads, clone sequences and assembly contigs with BWA‐MEM
no DOI — not checkedATLAS: Analysis Tools for Low‐depth and Ancient Samples
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carried a retraction notice at that time. It says nothing about the quality, findings,
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