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Inferring Variation in Copy Number Using High Throughput Sequencing Data in R

https://doi.org/10.3389/fgene.2018.00123
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Quality control and quality assurance in genotypic data for genome‐wide association studies
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An evaluation of the use of triploid Atlantic salmon (Salmo salar L.) in minimising the impact of escaped farmed salmon on wild populations
inferredcites →https://doi.org/10.1016/s0167-7799(00)01448-7openalex-snapshot
Less is better: new approaches for seedless fruit production
inferredcites →https://doi.org/10.1038/35066065openalex-snapshot
To err (meiotically) is human: the genesis of human aneuploidy
inferredcites →https://doi.org/10.1038/nature08358openalex-snapshot
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
inferredcites →https://doi.org/10.1038/nature16549openalex-snapshot
Schizophrenia risk from complex variation of complement component 4
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nrg.2017.26openalex-snapshot
The evolutionary significance of polyploidy
inferredcites →https://doi.org/10.1073/pnas.70.12.3321openalex-snapshot
Analysis of Gene Diversity in Subdivided Populations
inferredcites →https://doi.org/10.1093/bib/bbs086openalex-snapshot
A survey of tools for variant analysis of next-generation genome sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btm308openalex-snapshot
TASSEL: software for association mapping of complex traits in diverse samples
inferredcites →https://doi.org/10.1093/bioinformatics/btn129openalex-snapshot
adegenet : a R package for the multivariate analysis of genetic markers
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts146openalex-snapshot
CONTRA: copy number analysis for targeted resequencing
inferredcites →https://doi.org/10.1093/nar/gks003openalex-snapshot
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
inferredcites →https://doi.org/10.1101/gr.092981.109openalex-snapshot
Sensitive and accurate detection of copy number variants using read depth of coverage
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.114876.110openalex-snapshot
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
inferredcites →https://doi.org/10.1101/gr.126599.111openalex-snapshot
Assemblathon 1: A competitive assessment of de novo short read assembly methods
inferredcites →https://doi.org/10.1109/tac.1974.1100705openalex-snapshot
A new look at the statistical model identification
inferredcites →https://doi.org/10.1111/1755-0998.12549openalex-snapshot
vcfr : a package to manipulate and visualize variant call format data in R
inferredcites →https://doi.org/10.1111/1755-0998.12577openalex-snapshot
Linking genomics and population genetics with R
inferredcites →https://doi.org/10.1111/1755-0998.12613openalex-snapshot
Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping‐by‐sequencing data from natural populations
inferredcites →https://doi.org/10.1111/1755-0998.12636openalex-snapshot
Towards an integrated ecosystem of R packages for the analysis of population genetic data
inferredcites →https://doi.org/10.1111/1755-0998.12657openalex-snapshot
Detection of individual ploidy levels with genotyping‐by‐sequencing (GBS) analysis
inferredcites →https://doi.org/10.1111/j.0014-3820.2005.tb01814.xopenalex-snapshot
A STANDARDIZED GENETIC DIFFERENTIATION MEASURE
inferredcites →https://doi.org/10.1111/mec.13644openalex-snapshot
Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site‐associated markers
inferredcites →https://doi.org/10.1128/microbiolspec.funk-0051-2016openalex-snapshot
Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution
inferredcites →https://doi.org/10.1186/2047-217x-2-10openalex-snapshot
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
inferredcites →https://doi.org/10.1186/s12859-018-2128-zopenalex-snapshot
nQuire: a statistical framework for ploidy estimation using next generation sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1371/journal.pone.0059128openalex-snapshot
Comparative Studies of Copy Number Variation Detection Methods for Next-Generation Sequencing Technologies
inferredcites →https://doi.org/10.1534/g3.113.008995openalex-snapshot
The Reference Genome Sequence ofSaccharomyces cerevisiae: Then and Now
inferredcites →https://doi.org/10.1534/g3.116.029397openalex-snapshot
Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation
inferredcites →https://doi.org/10.17605/osf.io/zq879openalex-snapshot
Methods for calling ploidy or copy number variation in R
inferredcites →https://doi.org/10.32614/cran.package.rjagsopenalex-snapshot
rjags: Bayesian Graphical Models using MCMC
inferredcites →https://doi.org/10.3389/fgene.2013.00273openalex-snapshot
Copy-number changes in evolution: rates, fitness effects and adaptive significance
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.7312/nei-92038openalex-snapshot
Molecular Evolutionary Genetics
inferredcites →https://doi.org/10.7554/elife.00731openalex-snapshot
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine
inferredcites →https://doi.org/10.7717/peerj.3889openalex-snapshot
Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/tax.13176zenodo-depositor-declared
Altai Mountains – cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)
inferred← citeshttps://doi.org/10.1002/tpg2.20056openalex-snapshot
Making the most of all data: Combining non‐genotyped and genotyped potato individuals with HBLUP
inferred← citeshttps://doi.org/10.1007/s00122-018-3215-2openalex-snapshot
Modeling copy number variation in the genomic prediction of maize hybrids
inferred← citeshttps://doi.org/10.1093/botlinnean/boag081openalex-snapshot
Spatial genetic structure of the nomadic Vanilla trigonocarpa populations in Costa Rica reveals clonality and effective gene flow
inferred← citeshttps://doi.org/10.1093/g3journal/jkae258openalex-snapshot
Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim
inferred← citeshttps://doi.org/10.1093/isd/ixag017openalex-snapshot
Regionally localized population genetic structure of a non-native terrestrial isopod ( Porcellio spinicornis ) (Isopoda: Porcellionidae)
inferred← citeshttps://doi.org/10.1094/mpmi-08-24-0101-ropenalex-snapshot
Phytophthora cinnamomi Populations Affecting Avocado in California Show Low Differentiation, Phenotypic Variability, and Introductions from Mexico
inferred← citeshttps://doi.org/10.1094/phyto-12-18-0475-ropenalex-snapshot
Genetic Diversity of Verticillium dahliae Isolates From Mint Detected with Genotyping by Sequencing
inferred← citeshttps://doi.org/10.1094/phyto-12-18-0485-ropenalex-snapshot
Genotyping-by-Sequencing Reveals Fine-Scale Differentiation in Populations of Pseudoperonospora humuli
inferred← citeshttps://doi.org/10.1101/2021.12.12.472145openalex-snapshot
Combined Pan-, Population-, and Phylo-Genomic Analysis of Aspergillus fumigatus Reveals Population Structure and Lineage-Specific Diversity
inferred← citeshttps://doi.org/10.1101/827790openalex-snapshot
Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing
inferred← citeshttps://doi.org/10.1128/mbio.00326-20openalex-snapshot
Genome-Wide Increased Copy Number is Associated with Emergence of Dominant Clones of the Irish Potato Famine Pathogen Phytophthora infestans
inferred← citeshttps://doi.org/10.1128/mra.00896-19openalex-snapshot
Draft Genome Sequence of the Biofuel-Relevant Microalga Desmodesmus armatus
inferred← citeshttps://doi.org/10.1186/s12859-022-04685-zopenalex-snapshot
Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state
inferred← citeshttps://doi.org/10.1186/s43008-023-00109-6openalex-snapshot
Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001890openalex-snapshot
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination
inferred← citeshttps://doi.org/10.3389/fmicb.2020.00252openalex-snapshot
Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1341803openalex-snapshot
Genomic and transcriptomic analyses of Phytophthora cinnamomi reveal complex genome architecture, expansion of pathogenicity factors, and host-dependent gene expression profiles
inferred← citeshttps://doi.org/10.3390/plants11151919openalex-snapshot
Genotyping-by-Sequencing and Morphology Revealed the Role of Polyploidization and Hybridization in the Diversification of the Centaurea aspera L. Complex of Section Seridia (Juss.) DC. (Asteraceae)
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