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Reference: Oyola, SO, Otto, TD, Gu, Y et al., (2012). Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics, 13 (1), Article: 1.Citable link to this page:

 

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

Abstract: Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences.

Peer Review status:Peer reviewedPublication status:PublishedVersion:Publisher's version Funder: Wellcome Trust   Notes:file: :C$$:/Users/dominic/Dropbox/Refs/2012/Oyola et al._2012_Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.pdf:pdfkeywords: Base Composition,DNA-Directed RNA Polymerases,DNA-Directed RNA Polymerases: metabolism,Gene Library,Genetic Loci,Genome, Protozoan,High-Throughput Nucleotide Sequencing,High-Throughput Nucleotide Sequencing: methods,Plasmodium falciparum,Plasmodium falciparum: genetics,Polymerase Chain Reaction,Reproducibility of Results,Viral Proteins,Viral Proteins: metabolismpmid: 22214261Notes:© 2012 Oyola et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Bibliographic Details

Publisher: BioMed Central Ltd.

Publisher Website: http://www.biomedcentral.com/

Publisher: BioMed Central Ltd

Publisher Website: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3312816andtool=pmcentrezandrendertype=abstract

Journal: BMC Genomicssee more from them

Publication Website: http://www.biomedcentral.com/bmcgenomics/

Issue Date: 2012-1

pages:Article: 1Identifiers

Urn: uuid:5a11233c-f5fd-4872-b918-be8e5454b9a7

Source identifier: 322783

Eissn: 1471-2164

Doi: https://doi.org/10.1186/1471-2164-13-1

Issn: 1471-2164 Item Description

Type: Journal article;

Language: eng

Version: Publisher's versionKeywords: Plasmodium falciparum Viral Proteins Reproducibility of Results Polymerase Chain Reaction Gene Library Genome, Protozoan Genetic Loci Base Composition High-Throughput Nucleotide Sequencing DNA-Directed RNA Polymerases Tiny URL: pubs:322783

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Author: Oyola, SO - - - Otto, TD - - - Gu, Y - - - Maslen, G - - - Manske, M - - - Campino, S - - - Turner, DJ - - - Macinnis, B - - - Kw

Source: https://ora.ox.ac.uk/objects/uuid:5a11233c-f5fd-4872-b918-be8e5454b9a7



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