The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Special features of RAD Sequencing data: implications for genotyping
Open accessAbstract
Restriction site‐associated DNA Sequencing (RAD‐Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing‐by‐synthesis methods,RAD‐Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD‐Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD‐Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools.
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Cites
ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 2×
“2011) and SOAPdenovo (Li et al .”
Genome structural variation discovery and genotyping
Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630 · cited 1×
“For example, handling low depth or repeat loci are issues widely discussed elsewhere in the literature (DePristo et al. 2011; Nielsen et al. 2011), and missing alleles will also occur with structural variation (Alkan et al. 2011).”
BackgroundGenotype and SNP calling from next-generation sequencing data
Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2986 · Cited by 1,396
Cited by
Genotyping‐by‐sequencing in ecological and conservation genomics
Narum, S. R., Buerkle, C. A., Davey, J. W., Miller, M. R., & Hohenlohe, P. A. (2013) · Molecular Ecology · doi:10.1111/mec.12350 · Cited by 565
Self-citationHigh-Throughput Genomic Data in Systematics and Phylogenetics
Lemmon, E. M., & Lemmon, A. R. (2013) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-110512-135822 · Cited by 502
RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping
Ali, O. A., O’Rourke, S. M., Amish, S. J., Meek, M. H., Luikart, G., Jeffres, C., & Miller, M. R. (2016) · Genetics · doi:10.1534/genetics.115.183665 · Cited by 482
O'Leary, S. J., Puritz, J. B., Willis, S. C., Hollenbeck, C. M., & Portnoy, D. S. (2018) · Molecular Ecology · doi:10.1111/mec.14792 · Cited by 434
Mastretta‐Yanes, A., Arrigo, N., Alvarez, N., Jorgensen, T. H., Piñero, D., & Emerson, B. C. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12291 · Cited by 391
Metadata
- Authors
- Davey, J. W., Cezard, T., Fuentes‐Utrilla, P., Eland, C., Gharbi, K., & Blaxter, M. L.
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2012-10-30
- Volume
- 22
- Issue
- 11
- Pages
- 3151-3164
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W2102308328
- Cited by
- 343
- References
- 5
- FWCI
- 13.64
- Type
- journal article
- Language
- en
- Open access
- bronze
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