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Conference Paper: Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

TitleNext generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions
Authors
Issue Date2011
PublisherThe University of Hong Kong.
Citation
The 2011 Hong Kong Inter-University Biochemistry Postgraduate Symposium, Hong Kong, 11 June 2011. How to Cite?
AbstractThe rapid development of next generation sequencing (NGS) technology provides a new chance to extend the scale and resolution of genomic research. How to efficiently map millions of short reads to the reference genome and how to make accurate SNP calls are two major challenges in taking full advantage of NGS. In this article, we reviewed the current software tools for mapping and SNP calling, and evaluated their performance on samples from The Cancer Genome Atlas (TCGA) project. We found that BWA and Bowtie are superior to the other alignment tools in comprehensive performance, while SOAP2 has the fastest alignment speed and SHRiMP has the highest coverage. Furthermore, we showed that next-generation sequencing platform has significantly lower coverage and poorer SNP-calling performance in the CpG islands, promoter and 5’-UTR regions of the genome. NGS experiments targeting for these regions should have higher sequencing depth than the normal genomic region.
DescriptionPoster Presentation: P-H011
Symposium URL at http://www.biochem.hku.hk/postgraduate/symposium2011/
Persistent Identifierhttp://hdl.handle.net/10722/140076

 

DC FieldValueLanguage
dc.contributor.authorWang, Wen_US
dc.contributor.authorWei, Zen_US
dc.contributor.authorLam, TWen_US
dc.contributor.authorWang, JJen_US
dc.date.accessioned2011-09-23T06:06:20Z-
dc.date.available2011-09-23T06:06:20Z-
dc.date.issued2011en_US
dc.identifier.citationThe 2011 Hong Kong Inter-University Biochemistry Postgraduate Symposium, Hong Kong, 11 June 2011.en_US
dc.identifier.urihttp://hdl.handle.net/10722/140076-
dc.descriptionPoster Presentation: P-H011-
dc.descriptionSymposium URL at http://www.biochem.hku.hk/postgraduate/symposium2011/-
dc.description.abstractThe rapid development of next generation sequencing (NGS) technology provides a new chance to extend the scale and resolution of genomic research. How to efficiently map millions of short reads to the reference genome and how to make accurate SNP calls are two major challenges in taking full advantage of NGS. In this article, we reviewed the current software tools for mapping and SNP calling, and evaluated their performance on samples from The Cancer Genome Atlas (TCGA) project. We found that BWA and Bowtie are superior to the other alignment tools in comprehensive performance, while SOAP2 has the fastest alignment speed and SHRiMP has the highest coverage. Furthermore, we showed that next-generation sequencing platform has significantly lower coverage and poorer SNP-calling performance in the CpG islands, promoter and 5’-UTR regions of the genome. NGS experiments targeting for these regions should have higher sequencing depth than the normal genomic region.-
dc.languageengen_US
dc.publisherThe University of Hong Kong.-
dc.relation.ispartofHong Kong Inter-University Biochemistry Postgraduate Symposium, 2011en_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleNext generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regionsen_US
dc.typeConference_Paperen_US
dc.identifier.emailWang, W: weixin@hku.hken_US
dc.identifier.emailLam, TW: hresltk@hkucc.hku.hken_US
dc.identifier.emailWang, JJ: junwen@hku.hk-
dc.identifier.authorityWang, JJ=rp00280en_US
dc.identifier.authorityLam, TW=rp00135en_US
dc.description.naturepostprint-
dc.identifier.hkuros192434en_US
dc.publisher.placeHong Kong-
dc.description.otherThe 2011 Hong Kong Inter-University Biochemistry Postgraduate Symposium, Hong Kong, 11 June 2011.-

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