title: Effects of GC bias in next-generation-sequencing data on de novo genome assembly.
abstract: Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.
authors: Department of Engineering Science, National Cheng Kung University, Tainan, Taiwan.
authors: Yen-Chun
authors: YC
authors: Chen
authors: Tsunglin
authors: T
authors: Liu
authors: Chun-Hui
authors: CH
authors: Yu
authors: Tzen-Yuh
authors: TY
authors: Chiang
authors: Chi-Chuan
authors: CC
authors: Hwang
mesh_terms: D016477:Artifacts; D020862:GC Rich Sequence; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods* / Q000592:standards; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D012015:Reference Standards
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