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  A step-by-step guide to assemble a reptilian genome

Ullate-Agote, A., Chan, Y., & Tzika, A. (2017). A step-by-step guide to assemble a reptilian genome. In S. Guojun (Ed.), Methods in Molecular Biology. US: Springer.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0002-B089-C Version Permalink: https://hdl.handle.net/21.11116/0000-000A-5918-8
Genre: Book Chapter

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 Creators:
Ullate-Agote, A, Author
Chan, YF1, Author           
Tzika, AC, Author
Affiliations:
1Chan Group, Friedrich Miescher Laboratory, Max Planck Society, ou_3008688              

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 Abstract: Multiple technologies and software are now available facilitating the de novo sequencing and assembly of any vertebrate genome. Yet the quality of most available sequenced genomes is substantially poorer than that of the golden standard in the field: the human genome. Here, we present a step-by-step protocol for the successful sequencing and assembly of a high-quality snake genome that can be applied to any other reptilian or avian species. We combine the great sequencing depth and accuracy of short reads with the use of different insert size libraries for extended scaffolding followed by optical mapping. We show that this procedure improved the corn snake scaffold N50 from 3.7 kbp to 1.4 Mbp, currently making it one of the snake genomes with the longest scaffolds. Short guidelines are also given on the extraction of long DNA molecules from reptilian blood and the necessary modifications in DNA extraction protocols. This chapter is accompanied by a website ( www.reptilomics.org/stepbystep.html ), where we provide links to the suggested software, examples of input and output files, and running parameters.

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Language(s): eng - English
 Dates: 2017
 Publication Status: Issued
 Pages: 20
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1007/978-1-4939-7216-6_3
PMID: 28809013
 Degree: -

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Title: Methods in Molecular Biology
  Other : Methods Mol. Biol.
Source Genre: Series
 Creator(s):
Guojun , Sheng1, Editor
Affiliations:
1 Springer, New York, ou_persistent22            
Publ. Info: US : Springer
Pages: - Volume / Issue: 1650 Sequence Number: - Start / End Page: - Identifier: ISSN: 1064-3745
CoNE: https://pure.mpg.de/cone/journals/resource/954927725544

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Title: Avian and Reptilian Developmental Biology: Methods and Protocols
Source Genre: Book
 Creator(s):
Sheng, G, Editor
Affiliations:
-
Publ. Info: Totowa, NJ, USA : Human Press
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 47 - 67 Identifier: ISBN: 978-1-4939-7216-6