330    ◾    Index

SNP 135–136, 139–143

SnpEff 145, 148–151, 161

SNV 110, 114, 116

SOAP 65, 87

SOLiD 6, 8, 135, 156, 253

sonication 4, 214

SPAdes 92, 97–100, 102, 105–108,

315–316

splicing site 148, 164

SRA-toolkit 14–15, 70, 215, 265, 305

ssDNA 3, 5, 7, 9–10

STAR 58, 70–71, 76–78

stop codon 110, 143

stop-gain 143, 148

structural variant 113

suffix array 55, 57–60, 65, 72, 77–78, 86–87

suffix tree 55–58, 65, 87, 246

sulfurylase 5

SV 110

SW 46, 55, 65, 72–74, 326

tag 69–70, 80, 134, 215–216

tandem repeats 89

TATA box 164

TGS 8–9, 45, 85

third-generation sequencing 8

thymine 1–2, 13, 213, 247

TPM 175

transcription start site see TSS

transcripts per million see TPM

transition 109, 256–257

translocation 109–110

transversion 109

trie 11, 56, 65, 87

trimmomatic 42–47

triphosphate 4–5

TruSeq 97

TSS 144, 164, 233–238

ubiquitylation 213

UniFrac 261–263, 297, 300

untranslated region see UTR

UPGMA 261

Uracil 1

USEARCH 255

UTR 144, 148

variant call format see VCF

variant calling 113–116

Variant Quality Score Recalibration see VQSR

VCF 110–113, 115–116

vertexes 91

virion 1–2

virus 99, 116, 253

volcano 199–200, 208–209

VQSR 139–141

VSEARCH 258–259, 278, 280–282

Watson, James 3

WPGMA 261