Contents ◾ vii
Chapter 3 ◾ De Novo Genome Assembly
89
3.1 INTRODUCTION TO DE NOVO GENOME ASSEMBLY
89
3.1.1
Greedy Algorithm
90
3.1.2
Overlap-Consensus Graphs
90
3.1.3
De Bruijn Graphs
91
3.2 EXAMPLES OF DE NOVO ASSEMBLERS
93
3.2.1
ABySS
93
3.2.2
SPAdes
97
3.3 GENOME ASSEMBLY QUALITY ASSESSMENT
99
3.3.1
Statistical Assessment for Genome Assembly
100
3.3.2
Evolutionary Assessment for De Novo Genome Assembly
103
3.4 SUMMARY
106
REFERENCES
107
Chapter 4 ◾ Variant Discovery
109
4.1 INTRODUCTION TO GENETIC VARIATIONS
109
4.1.1
VCF File Format
110
4.1.2. Variant Calling and Analysis
113
4.2 VARIANT CALLING PROGRAMS
114
4.2.1
Consensus-Based Variant Callers
114
4.2.1.1 BCF Tools Variant Calling Pipeline
115
4.2.2
Haplotype-Based Variant Callers
125
4.2.2.1 FreeBayes Variant Calling Pipeline
127
4.2.2.2 GATK Variant Calling Pipeline
129
4.3 VISUALIZING VARIANTS
143
4.4 VARIANT ANNOTATION AND PRIORITIZATION
143
4.4.1
SIFT
145
4.4.2
SnpEff
148
4.3.3
ANNOVAR
151
4.3.3.1 Annotation Databases
153
4.3.3.2 ANNOVAR Input Files
156
4.5 SUMMARY
160
REFERENCES
161