v

Contents

Preface, xiii

Author, xvii

Chapter 1    ◾    Sequencing and Raw Sequence Data Quality Control

1

1.1 NUCLEIC ACIDS

1

1.2 SEQUENCING

3

1.2.1

First-Generation Sequencing

3

1.2.2

Next-Generation Sequencing

4

1.2.2.1 Roche 454 Technology

5

1.2.2.2 Ion Torrent Technology

6

1.2.2.3 AB SOLiD Technology

6

1.2.2.4 Illumina Technology

7

1.2.3

Third-Generation Sequencing

8

1.2.3.1 PacBio Technology

9

1.2.3.2 Oxford Nanopore Technology

10

1.3 SEQUENCING DEPTH AND READ QUALITY

11

1.3.1

Sequencing Depth

11

1.3.2

Base Call Quality

11

1.4 FASTQ FILES

13

1.5 FASTQ READ QUALITY ASSESSMENT

18

1.5.1

Basic Statistics

23

1.5.2

Per Base Sequence Quality

24

1.5.3

Per Tile Sequence Quality

25

1.5.4

Per Sequence Quality Scores

28

1.5.5

Per Base Sequence Content

28

1.5.6

Per Sequence GC Content

28

1.5.7

Per Base N Content

30