Special features of RAD Sequencing data: implications for genotyping.
John W. Davey,Timothee Cezard,Pablo Fuentes-Utrilla,Cathlene Eland,Karim Gharbi,Mark Blaxter +5 more
TLDR
It is shown 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, and that most RAD loci will be accurately genotyped by existing tools.Abstract:
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.read more
Citations
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Stacks: an analysis tool set for population genomics
Julian M. Catchen,Paul A. Hohenlohe,Paul A. Hohenlohe,Susan Bassham,Angel Amores,William A. Cresko +5 more
TL;DR: The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Journal ArticleDOI
Harnessing the power of RADseq for ecological and evolutionary genomics
TL;DR: This Review provides a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
Journal ArticleDOI
Genotyping‐by‐sequencing in ecological and conservation genomics
TL;DR: This special issue on ‘Genotyping-by-Sequencing in Ecological and Conservation Genomics’ represents a diverse set of empirical and theoretical studies that demonstrate both the utility and some of the challenges of GBS in ecological and conservation genomics.
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High-Throughput Genomic Data in Systematics and Phylogenetics
TL;DR: This review presents recent advances in laboratory methods for collection of high-throughput phylogenetic data and challenges and constraints for phylogenetic analysis of these data, and offers recommendations for the most promising protocols and data-analysis workflows currently available.
Journal ArticleDOI
Lost in parameter space: A road map for Stacks
TL;DR: Using three empirical RAD‐seq datasets, a method for optimising a de novo assembly of loci using stacks is demonstrated and the 80% rule is presented as a generally effective method to select the core parameters for stacks.
References
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