Title Page

Contents

ABSTRACT 8

Ⅰ. Introduction 10

Ⅱ. Material and Methods 12

2.1. DNA extraction and NGS sequencing 12

2.2. Bioinformatic data analysis 12

2.2.1. Complete genome construction 12

2.2.2. Performance comparison in polishing step 13

2.2.3. Antibiotic resistance gene detection 13

2.2.4. Statistical analysis 14

Ⅲ. Results 18

3.1. Sequencing results generated by each NGS platforms 18

3.2. General characteristic of the E.coli complete genome 18

3.3. Minimum depth coverage required to polish the complete E.coli genome 19

3.4. Number of CDS in the complete genome polished at different coverage depths 19

3.5. Comparison of antibiotic resistance gene detection 19

Ⅳ. Discussion 31

References 34

Abstract (in Korean) 41

〈Table 1〉 The list of designed primer pairs to determine genetic variants between the polished genomes by 200X Illumina and 200X MGI data sets. 16

〈Table 2〉 Raw data generated by each NGS platform. 20

〈Table 3〉 Input DNA quantity, cost, and time consumed for each NGS sequencing platform in this study. 21

〈Table 4〉 The characteristic of genetic variants between draft genomes separately polished with 200X Illumina and 200X MGI subsampled data... 22

〈Table 5〉 The general characteristic of the corrected E.coli complete genome 24

〈Figure 1〉 The workflow of DNA extraction, bacterial complete genome construction, and resistance gene detection in this study. 15

〈Figure 2〉 Linear aggression of variant numbers per depth difference in E.coli genome 25

〈Figure 3〉 The boxplot of number of CDS annotated in the E. coli complete genomes polished at different coverage depths 28

〈Figure 4〉 The heatmap of antibiotic resistance gene detected in contigs de novo assembled from raw data per depth difference generated from... 29