Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-04

AUTHORS

Iwanka Kozarewa, Zemin Ning, Michael A Quail, Mandy J Sanders, Matthew Berriman, Daniel J Turner

ABSTRACT

Amplification artifacts introduced during library preparation for the Illumina Genome Analyzer increase the likelihood that an appreciable proportion of these sequences will be duplicates and cause an uneven distribution of read coverage across the targeted sequencing regions. As a consequence, these unfavorable features result in difficulties in genome assembly and variation analysis from the short reads, particularly when the sequences are from genomes with base compositions at the extremes of high or low G+C content. Here we present an amplification-free method of library preparation, in which the cluster amplification step, rather than the PCR, enriches for fully ligated template strands, reducing the incidence of duplicate sequences, improving read mapping and single nucleotide polymorphism calling and aiding de novo assembly. We illustrate this by generating and analyzing DNA sequences from extremely (G+C)-poor (Plasmodium falciparum), (G+C)-neutral (Escherichia coli) and (G+C)-rich (Bordetella pertussis) genomes. More... »

PAGES

291

Journal

TITLE

Nature Methods

ISSUE

4

VOLUME

6

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth.1311

DOI

http://dx.doi.org/10.1038/nmeth.1311

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1023653905

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19287394


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