Demystifying the RAD fad

Molecular Ecology

Volumn 23, Issue 24, 2014, Pages 5937-5942

  Puritz, Jonathan B ^a   Matz, Mikhail V ^b   Toonen, Robert J ^c   Weber, Jesse N ^d   Bolnick, Daniel I ^d   Bird, Christopher E ^a  

^a TEXAS A AND M UNIVERSITY CORPUS CHRISTI   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c UNIVERSITY OF HAWAII   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

genomics; next generation sequencing; population; restriction; restriction site associated DNA

Indexed keywords

ARTIFACT; COMPARATIVE STUDY; DNA SEQUENCE; METAGENOMICS; PROCEDURES; RESTRICTION MAPPING; STATISTICAL BIAS;

ARTIFACTS; BIAS (EPIDEMIOLOGY); METAGENOMICS; RESTRICTION MAPPING; SEQUENCE ANALYSIS, DNA;

EID: 84919725058     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12965     Document Type: Review

References (23)

1. Aird D, Ross MG, Chen WS, et al,. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biology, 12, R18.
2. Andrews KR, Luikart G, (2014) Recent novel approaches for population genomics data analysis. Molecular Ecology, 23, 1661-1667.
3. Arnold B, Corbett-Detig RB, Hartl D, et al,. (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, 22, 3179-3190.
4. van der Auwera GA, Carneiro MO, Hartl C, et al,. (2013) From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics. 11:11.10:11.10.1-11.10.33.
5. Baird NA, Etter PD, Atwood TS, et al,. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One, 3, e3376.
6. Baxter SW, Davey JW, Johnston JS, et al,. (2011) Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One, 6, e19315.
7. Casbon JA, Osborne RJ, Brenner S, et al,. (2011) A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Research, 39, e81.
8. Catchen JM, Amores A, Hohenlohe P, et al,. (2011) Stacks: Building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1, 171-182.
9. Davey JW, Cezard T, Fuentes-Utrilla P, et al,. (2013) Special features of RAD Sequencing data: implications for genotyping. Molecular Ecology, 22, 3151-3164.
10. DePristo MA, Banks E, Poplin R, et al,. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics, 43, 491-498.
11. Elshire RJ, Glaubitz JC, Sun Q, et al,. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One, 6, e19379.
12. Garrison E, Marth G., (2012) Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN].
13. Gautier M, Foucaud J, Gharbi K, et al,. (2013) Estimation of population allele frequencies from next-generation sequencing data: Pool-versus individual-based genotyping. Molecular Ecology, 22, 3766-3779.
14. Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y, (2012) The effect of strand bias in Illumina short-read sequencing data. BMC Genomics, 13, 666.
15. Miller MR, Dunham JP, Amores A, et al,. (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17, 240-248.
16. Oyola SO, Otto TD, Gu Y, et al,. (2012) Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics, 13, 1.
17. Peterson BK, Weber JN, Kay EH, et al,. (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One, 7, e37135.
18. Poland JA, Brown PJ, Sorrells ME, et al,. (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One, 7, e32253.
19. Puritz JB, Hollenbeck CM, Gold JR, (2012) dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ, 2: e431 doi: 10.7717/peerj.431.
20. Sonah H, Bastien M, Iquira E, et al,. (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One, 8, e54603.
21. Stolle E, Moritz RFA, (2013) RESTseq-efficient benchtop population genomics with RESTriction Fragment SEQuencing. PLoS One, 8, e63960.
22. Toonen RJ, Puritz JB, Forsman ZH, et al,. (2013) ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ, 1, e203.
23. Wang S, Meyer E, McKay JK, et al,. (2012) 2b-RAD: a simple and flexible method for genome-wide genotyping. Nature methods, 9, 808-810.