Paired-end RAD-seq for de novo assembly and marker design without available 
reference

Willing, E-M; Hoffmann, M; Klein, JD; Weigel, D; Dreyer, C

doi:10.1093/bioinformatics/btr346

Item

ITEM ACTIONSEXPORT

Add to Basket

Local TagsRelease HistoryDetailsSummary

Released

Journal Article

Paired-end RAD-seq for de novo assembly and marker design without available reference

MPS-Authors

/persons/resource/persons129123

Willing, E-M
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

/persons/resource/persons272554

Hoffmann, M
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

/persons/resource/persons85266

Weigel, D
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

/persons/resource/persons272562

Dreyer, C
Department Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

External Resource

No external resources are shared

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

There are no public fulltexts stored in PuRe

Supplementary Material (public)

There is no public supplementary material available

Citation

Willing, E.-M., Hoffmann, M., Klein, J., Weigel, D., & Dreyer, C. (2011). Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics, 27(16), 2187-2193. doi:10.1093/bioinformatics/btr346.

Cite as: https://hdl.handle.net/21.11116/0000-000A-D890-F

Abstract

Motivation: Next-generation sequencing technologies have facilitated the study of organisms on a genome-wide scale. A recent method called restriction site associated DNA sequencing (RAD-seq) allows to sample sequence information at reduced complexity across a target genome using the Illumina platform. Single-end RAD-seq has proven to provide a large number of informative genetic markers in reference as well as non-reference organisms.

Results: Here, we present a method for de novo assembly of paired-end RAD-seq data in order to produce extended contigs flanking a restriction site. We were able to reconstruct one-tenth of the guppy genome represented by 200-500 bp contigs associated to EcoRI recognition sites. In addition, these contigs were used as reference allowing the detection of thousands of new polymorphic markers that are informative for mapping and population genetic studies in the guppy.

Availability: A perl and C++ implementation of the method demonstrated in this article is available under http://guppy.weigelworld.org/weigeldatabases/radMarkers/ as package RApiD.