About: Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform

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About: Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform
Creator	Fernandez, Stefan Klungthong, Chonticha Manasatienkij, Wudtichai Huang, Angkana Chookajorn, Thanat Batty, Elizabeth Chantratita, Wasun Jiaranai, Poramate Jones, Anthony Joonlasak, Khajohn Kochakarn, Theerarat Kotanan, Namfon Kümpornsin, Krittikorn Panthan, Bhakbhoom Pasomsub, Ekawat Rakmanee, Kingkan Sensorn, Insee Sungkanuparph, Somnuek Wangwiwatsin, Arporn Watthanachockchai, Treewat
Source	BioRxiv
abstract	Genomic surveillance has a key role in tracking the ongoing COVID-19 pandemic, but information on how different sequencing library preparation approaches affect the data produced are lacking. We compared three library preparation methods using both tagmentation (Nextera XT and Nextera Flex) and ligation-based (KAPA HyperPrep) approaches on both positive and negative samples to provide insights into any methodological differences between the methods, and validate their use in SARS-CoV-2 amplicon sequencing. We show that all three library preparation methods allow us to recover near-complete SARS-CoV-2 genomes with identical SNP calls. The Nextera Flex and KAPA library preparation methods gave better coverage than libraries prepared with Nextera XT, which required more reads to call the same number of genomic positions. The KAPA ligation-based approach shows the lowest levels of human contamination, but contaminating reads had no effect on the downstream analysis. We found some examples of library preparation-specific differences in minority variant calling. Overall our data shows that the choice of Illumina library preparation method has minimal effects on consensus base calling and downstream phylogenetic analysis, and suggests that all methods would be suitable for use if specific reagents are difficult to obtain.
has issue date	2020-06-16(xsd:dateTime)
bibo:doi	10.1101/2020.06.16.154286
has license	biorxiv
sha1sum (hex)	d3f7005dccdf8cdbcfabaeff216897d82cb94200
schema:url	https://doi.org/10.1101/2020.06.16.154286
resource representing a document's title	Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform
schema:publication	bioRxiv
resource representing a document's body	covid:d3f7005dccdf8cdbcfabaeff216897d82cb94200#body_text
is schema:about of	named entity 'library' named entity 'SNP' named entity 'minority' named entity 'positions' named entity 'produced' named entity 'contaminating' named entity 'effects' covid:arg/d3f7005dccdf8cdbcfabaeff216897d82cb94200 named entity 'library' named entity 'specific' named entity 'samples' named entity 'preparation' named entity 'ongoing' named entity 'preparation' named entity 'call' named entity 'SARS-CoV-2' named entity 'number' named entity 'ligation' named entity 'library preparation' named entity 'Nextera' named entity 'KAPA' named entity 'ligation' named entity 'library preparation' named entity 'library preparation' named entity 'amplicon sequencing' named entity 'SARS' named entity 'Illumina MiSeq' named entity 'Invitrogen' named entity 'Nextera' named entity 'SARS-CoV-2' named entity 'multiplex PCR' named entity 'reverse transcriptase' named entity 'Illumina' named entity 'KAPA' named entity 'amplicons' named entity 'ligation' named entity 'number of reads' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'Nextera' named entity 'amplicon' named entity 'Nextera' named entity 'negative control' named entity 'Nextera' named entity 'amplicon' named entity 'Illumina' named entity 'minuscule' named entity 'amplicons' named entity 'March 2020' named entity 'quality score' named entity 'cDNA' named entity 'SNPs' named entity 'library preparation' named entity 'genome' named entity 'Nextera' named entity 'Illumina sequencing' named entity 'SNPs' named entity 'library preparation' named entity 'primers' named entity '250,000' named entity 'clinical diagnostic' named entity 'Thailand' named entity 'Nextera' named entity 'SNPs' named entity 'denature'

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