328    ◾    Index

EBI 50, 265

EdgeR 174–175

electrophoresis 3–4

entropy 126

epigenetics 4–5, 9, 11, 45, 49, 64, 86

eQTL 165–166

escherichia coli 20, 49, 94

ETE toolkit 298

Eulerian path 90, 92, 107

evenness 261–262

exon 2, 52, 63, 77, 144

Faith’s phylogenetic diversity 261–262, 297

Fastp 44, 46–47

Fastqc 18–23, 32, 36–44

Fasttree 297–298

feature table 258, 261, 278, 280–283

FeatureCounts 173, 212

Ferragina-Manzini 311

flow cell 4, 7–10, 14, 18, 25–27, 66, 134

FM-index 56, 62, 71, 75, 86–87

FPKM 174–175, 206–207, 210

frameshift 110, 143–144, 148, 150, 159

FreeBayes 114, 127, 129, 143

Full-text Minute-space see FM-index

fungi 49, 97, 303

fusion 165–166, 211

GATK 66, 114, 127, 129–132,

134–143, 160

GC content 20, 23–24, 28–29, 46–47

GenBank 50–52, 325

gene expression 163–167

gene ontology see GO

gene transcription 163–164, 218, 241

gene transfer format see GTF

General Feature Format see GFF

genetic drift 114

genetic mosaicism 113

Genome Reference Consortium see GRC

Genome Variant Call Format see gVCF

GFF 51–52

ggplot2 104

Gilbert, Walter 3

global sequence alignment 55

GO 66, 165, 202–203, 211–212, 239–241, 250

graphviz 95

GRC 50

greedy 90–91, 107, 255, 312

greengenes database 255, 281, 291

GTF 51–53

guanine 1–2, 13, 213, 247

gVCF 130, 137–138

Hamiltonian path 90–92, 107

Hamming distance 65, 255, 257, 260

haplotype 83, 104, 112, 114, 125–127

HaplotypeCaller 114, 130, 137

hard filtering 141–142

hashing xiv 65, 93

hash table 65, 86, 148

heatmap 25, 193–194, 200–202, 233, 318

helicase 3

heuristic clustering 255

hierarchical clustering 193, 255

high-throughput sequencing see HTS

histone 213, 216–217, 235–236, 243

HMMER 104, 323

homology 144, 251

HTS 13, 34, 45, 69–70

HTSeq-count 173–174, 210

hydroxyl 5, 7

Icarus 102, 104

iGenomes 169

IGV 142–143

InDel 114, 116, 121

insertion 63, 68–70

insertion-deletion see InDel

Integrated Genomics Viewer see IGV

Ion Torrent 6–7, 97–98

IQR 24

Jaccard distance 261–262

Jukes-Cantor 260

k-mers 33, 65, 91–93, 97, 107

Kaiju 311–312, 326

KEGG 165, 202–203, 211–212, 239, 241–242, 250

Kraken 311, 326

Kruskal-Wallis 300

Kyoto Encyclopedia of Genes and Genomes see

KEGG

L50 96, 102–103, 107

lactose operon 164

Levenshtein distance 65, 257

LG50 96

local sequence alignment 55, 258

locus 90, 172

logo 245, 249

lookup table 62–63

MAFFT 297–298

MAG 304

manifest file 268–269, 274–275

Maxam, Allan M. 3

MaxBin 304, 321, 326