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

Scientific Reports
Weixin WangJunwen Wang

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.

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Datasets Mentioned

BETA
SRS004141
SRX006310

Methods Mentioned

BETA
RNA-seq

Software Mentioned

bowtie
Varscan
MAQ
RepMask
BLAST
SNP
SeqMap
SNVMix
PolyBayes
Genome Analysis Toolkit ( GATK )

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