Genome Polishing of Nanopore-Only Assembly Using Coding Sequences

• Main Authors: HUNG, YU-KAI, 洪裕凱
• Other Authors: Huang, Yao-Ting
• Format: Others
• Language: en_US
• Published: 2019
• Online Access: http://ndltd.ncl.edu.tw/handle/9r9vu4

碩士 === 國立中正大學 === 資訊工程研究所 === 107 === Third-generation sequencing (TGS) produces longer reads, unbiased coverage, and faster sequencing speed in comparison with next-generation sequencing (NGS). Genome assembly based on TGS can usually assemble complete genome but its accuracy is lower than NGS assembly due to high error rate. Although hybrid NGS and TGS can generate complete and high-quality genomes, the sequencing cost is too high to be practical. This thesis aims to polish Oxford Nanopore (ONT)-assembled genomes using TGS reads only. By using the conservation of coding sequence (CDS) across bacterial species, we develop a suite of polishing methods for correcting indel errors leading to frameshift. The polished genome can achieve 97-100\% completeness, which significantly outperform previous polishing methods (65-90\%). The remaining uncorrected errors are mainly due to incompleteness of CDS in the current database, which can be improved as more sequencing data are collected in the future.