Abstract
Stacksbinder (available at https://ps.agr.ryukoku.ac.jp/stacksbinder/) is a web-based tool for summarizing the output of software Stacks, which is widely used to analyze restriction site-associated DNA sequencing (RAD-Seq) data. Although summarization is an essential step in RAD-Seq analysis, no specific tools exist for summarizing and visualizing these data. Stacksbinder generates a summary report by using files exported from Stacks. The report is HTML-based and easy to browse in any environment. It consists of plots and tables containing information that can be used to assess the quality of experiments and determine the filtering of single nucleotide polymorphisms.
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References
Baird NA, Etter PD, Atwood TS, Curry MC, Shiver AL, Lewis AZ, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376. https://doi.org/10.1371/journal.pone.0003376
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140. https://doi.org/10.1111/mec.12354
Chattopadhyay B, Garg KM, Ramakrishnan U (2014) Effect of diversity and missing data on genetic assignment with RAD-Seq markers. BMC Res Notes 7:841. https://doi.org/10.1186/1756-0500-7-841
Eaton DAR, Ree RH (2013) Inferring phylogeny and introgression using RAD-Seq data: an example from flowering plants (Pedicularis: Orobanchaceae). Syst Biol 62:689–706. https://doi.org/10.1093/sysbio/syt032
Elshire RJ, Glaubitz JC, Qi S, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. https://doi.org/10.1371/journal.pone.0019379
Huang H, Knowles LL (2016) Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD-Sequences. Syst Biol 65:357–365. https://doi.org/10.1093/sysbio/syu046
Rubin BER, Ree RH, Moreau CS (2012) Inferring phylogenies from RAD-Sequence data. PLoS ONE 7:e33394. https://doi.org/10.1371/journal.pone.0033394
Acknowledgements
We thank Fumie Kobayashi, Satoko Kondo, Naomi Niwa, Motohiro Mihara, Satoshi Ohshima, and Lina Kawaguchi for their assistance. This work was supported by the Research Institute for Food and Agriculture of Ryukoku University, JST CREST (Grant Number, JPMJCR15O2), JST ACCEL (Grant Number, JPMJAC1403), and JSPS KAKENHI (Grant Numbers, JP16H06171 and JP16H01473) to A.J.N.
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Yasugi, M., Tezuka, A. & Nagano, A.J. Stacksbinder: online tool for visualizing and summarizing Stacks output to aid filtering of SNPs identified using RAD sequencing. Conservation Genet Resour 12, 1–3 (2020). https://doi.org/10.1007/s12686-018-1050-z
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DOI: https://doi.org/10.1007/s12686-018-1050-z