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

Weixin Wang, Zhi Wei, Tak Wah Lam, Junwen Wang

Research output: Contribution to journalReview article

57 Scopus citations

Abstract

The 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 better than the other alignment tools in comprehensive performance for Illumina platform, while NovoalignCS showed the best overall performance for SOLiD. 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.

Original languageEnglish (US)
Article number55
JournalScientific Reports
Volume1
DOIs
StatePublished - 2011
Externally publishedYes

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ASJC Scopus subject areas

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