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RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms



RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms



Methods in Molecular Biology 888: 135-151



Restriction-site Associated DNA (RAD) markers are rapidly becoming a standard for SNP discovery and genotyping studies even in organisms without a sequenced reference genome. It is difficult, however, to identify genes nearby RAD markers of interest or move from SNPs identified by RAD to a high-throughput genotyping assay. Paired-end sequencing of RAD fragments can alleviate these problems by generating a set of paired sequences that can be locally assembled into high-quality contigs up to 1 kb in length. These contigs can then be used for SNP identification, homology searching, or high-throughput assay primer design. In this chapter, we offer suggestions on how to design a RAD paired-end (RAD-PE) sequencing project and the protocol for creating paired-end RAD libraries suitable for Illumina sequencers.

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Accession: 055332765

Download citation: RISBibTeXText

PMID: 22665280

DOI: 10.1007/978-1-61779-870-2_9



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