327
Index
16S rRNA gene 253, 260, 263
ABySS 92–96
acetylation 213
adaptor 4–9, 13, 18
adaptor dimer 18, 31–33, 46, 218
adenine 1–2, 13
adenosine triphosphate 5
alpha diversity 261–262, 299
alternative splicing 164–165, 172
ammonium persulfate 5
amplicon 253–257
ANNOVAR 145, 151–159, 161
archaea 49
ASCII 12, 14, 23, 67–68
assembly-free 304–305, 310–311, 325
Augustus 104
bacteria 49, 97, 105, 160, 253–254, 303, 325
bacteriophage 3, 46
base caller 11
base calling 6, 9, 11, 23, 85, 135, 256
Base Quality Score Recalibration see BQSR
base substitution 109–110, 114, 160
Basic Local Alignment Search Tool see BLAST
BCFTools 84–85
beta diversity 261–263, 289, 298–300
binning 304–305, 321–326
BioProject 20, 271–272, 274
BioPython 104
BLAST 55, 104, 146, 258–259, 287
Bowtie 58, 70–71, 75, 87, 215
BQSR 130, 135–139
Bray-Curtis distance 261
Burrows-Wheeler transform see BWT
BUSCO 100, 103–108
BWA 58, 70–75
BWA-backtrack 72, 74
BWA-MEM 72–74, 168
BWA-SW 72, 74
BWT 56, 58–63, 65, 71–72, 75, 86
CD-HIT 255
centrifuge 311, 313–315, 326
CheckM 323–324, 326
chimeric 77, 81, 86, 172, 284
chimeric read 81, 172, 284
ChIP-Seq 214–217
ChIPseeker 230, 236, 251
chromatin 213–215
chromatin immunoprecipitation see ChIP-Seq
chromatin remodeling 213
chromatography 3
CIGAR string 67–68, 82, 86
circular consensus sequences 9
CLARK 311, 326
closed-reference 255, 278, 280–282, 289, 301
clustering 193–194, 254–255, 257–258
CNV 109–110
consensus sequence 83, 85, 89–92, 114–115, 160
contig 83, 89–91, 93–100
copy number variation see CNV
coverage 89–91
Crick, Francis 3
Crohn’s disease 144
cytogenetic bands 151, 154
cytosine 1–2, 13, 213, 247
de Bruijn 90–93, 97, 107–108, 126, 137, 315
de novo 89–95, 97–101, 103–105, 297–298
de novo clustering 255, 280, 282, 285, 290, 301
deep sequencing 89–90, 107
defline 17, 51, 54
deletion 68–70, 82, 86, 109–112
dereplication 279–281
DESeq 174, 204, 210, 212
DGEList 182–184
differential expression 165–166, 176–177, 180, 185
DNA ligase 6
DOT language 95
double-stranded DNA see dsDNA
dsDNA 9
dynamic programing 55