INDE X
記号・数字%（シェルプロンプト）........................................................45--add_ggb オプション（phylophlan_metagenomic）........................................................................................139--annot オプション（graphlan_annotate.py）......143--cleaning-rounds オプション（megahit）............. 130--config オプション（dfast）......................................... 164--db_aa diamond オプション（phylophlan_
write_config_file）....................................................141--diversity オプション（phylophlan）........................142--size オプション（graphlan_annotate.py）...........143

alpha-rarefaction コマンド（qiime）..........................71--taxa オプション（gstk.pl）............................... 103, 104

alpha コマンド（qiime）...................................................73--tree1 fasttree オプション（phylophlan_write_
config_file）.................................................................141--tree2 raxml オプション（phylophlan_write_
config_file）.................................................................141--trim trimal オプション（phylophlan_write_

Amazon Web Service...................................................24
Amazon マシンイメージ....................................................27
AMI.......................................................................................27

config_file）.................................................................141

Amplicon Sequence Variant.....................................57--trimmomatic オプション（kneaddata）................128

Anaconda...........................................................10, 14, 45--trim オプション（phylophlan）.................................142

Anaconda - アップデート................................................ 18--use_locustag_as_gene_id オプション（dfast）

Anaconda - インストール................................................ 14--dpi オプション（graphlan_annotate.py）............143....................................................................................... 166

ANCOM.......................................................................77, 78--force オプション（gstk.pl）.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104--use_prodigal オプション（dfast）...........................162

ancom コマンド（qiime）................................................78--format オプション（graphlan_annotate.py）.....143--version オプション.........................................................22

ANI..................................................................................... 158--genome オプション（dfast）......................................162-a オプション（seqkit stats）........................................132

ANI 値.................................................................................139--input オプション（kneaddata）................................128-c オプション（conda）...................................................126

Ansible（プロビジョニング）........................................... 41--in オプション（gstk.pl）.............................................. 104-d amphora2 オプション（graphlan_annotate.py）

ARSA................................................................................. 195........................................................................................142

Assembly データベース................................................ 195-d phylophlan オプション（phylophlan）...............142

ASV.......................................................................................57-i オプション（DAS_Tool）.............................................137

ASV 数の分布...................................................................... 74--metagenome オプション（dfast）.......................... 166-M オプション（seqkit seq）.........................................133

ASV の種類..........................................................................71--metagenome オプション（prokka）...................... 140-m オプション（seqkit seq）.........................................133

average nucleotide identity................................... 158--meta オプション（spades.py）.................................132-m オプション（spades.py）..........................................131

awk スクリプト................................................................ 168--min-contig-length オプション（megahit）.......... 130-s オプション（spades.py）...........................................131

AWS......................................................................................24--msa mafft オプション（phylophlan_write_--isolates オプション（spades.py）............................132--map_aa diamond オプション（phylophlan_
write_config_file）....................................................141-t オプション（spades.py）............................................131

AWS EC2............................................................................25

config_file）.................................................................141-v interactive オプション（KEGG-decoder）......... 168

AWS EFS.............................................................................30--n-merging-threads オプション（gstk.pl）........... 104>（リダイレクト）................................................................. 51--n-search-tasks オプション（gstk.pl）................... 104（| パイプ）.............................................................................. 51--p-level オプション（qiime）.........................................67

16S rRNA....................................................................44, 98--p-max-depth オプション（qiime）............................71

16S rRNA 遺伝子...............................................................86

Bandage...........................................................................132--p-trim-left-f オプション（qiime）................................59

16S rRNA 参照配列データベース....................................48

BBtools.............................................................................129B--p-trim-left-r オプション（qiime）...............................59

16S rRNA の全長シークエンス........................................98

beta-group-significance コマンド（qiime）.............75--p-trunc-len-f オプション（qiime）..............................59

16S アンプリコン解析......................................................113

Binned アセンブリ......................................................... 183--p-trunc-len-r オプション（qiime）.............................59

515F/806R.........................................................................48--presets meta-large オプション（megahit）........ 130--presets meta-sensitive オプション（megahit）

Binned メタゲノム........................................................... 196
binning..............................................................................133A

bin 配列..............................................................................131--reference オプション（dfast）.................................. 163

add-pseudocount コマンド（qiime）.........................78

Bioconda.....................................................................10, 14--rep-taxa オプション（gstk.pl）...................... 103, 104align-to-tree-mafft-fasttree コマンド（qiime）......71

モックコミュニティ...........................................................126--search_engine blast オプション（DAS_Tool）...137

alpha-group-significance コマンド（qiime）...........73

bioconda チャネル.........................................................126....................................................................................... 130

230

Amazon Elastic File System.......................................30
Amazon ElasticCompute Cloud..............................25

メタゲノムデータ解析

bin 配列の品質評価規格................................................ 148

16Sも! ショットガンも! ロングリードも! 菌叢解析が得意になる凄技レシピ

biom コマンド（qiime）....................................................82

DADA2 実行結果..............................................................63

bioperl............................................................................. 140

DAS_Tool........................................................................ 136

F

BioProject................................................................49, 185

datamash_reverse.......................................................118

Faith PD.............................................................................. 74

BioProject の登録.......................................................... 185

DDBJ....................................................................... 153, 158

family-level genome bins..........................................139

BioSample...................................................................... 185

DDBJ Sequence Read Archive.....................182, 213

FAST5 データ.................................................................. 108

BioSample の登録......................................................... 186

DDBJ センター.................................................................182

FASTA 形式.......................................................................155

BLAST................................................................64, 82, 163

Deblur.................................................................................80

fasterq-dump コマンド................................................... 51

BMI.................................................................................... 224

demux ファイル..................................................................83

fastp...........................................................................89, 127

BMock12..........................................................................126

denoise-paired コマンド（qiime）........................59, 61

FASTQ...............................................................................128

Bowtie 2...........................................................................128

DFAST.................................................................... 153, 194

FASTQ 16S Workflow................................................ 106

brew コマンド...................................................................102

DFAST_core....................................................................159

fastqc コマンド................................................................127

DFAST ウェブサービス................................................... 154

FASTQ ファイル - インポート............................... 54

DFAST - インストール.................................................... 160

FASTQ ファイル - ダウンロード............................. 51

Digital Object Identifier........................................... 200

FASTQ ファイル - 複数回のラン. ........................... 82

cat コマンド......................................................................... 51

Docker.............................................................. 10, 15, 148

FastTree2.........................................................................141

centered log ratio..........................................................78

Docker Desktop............................................................. 15

Feature.....................................................................58, 194

Chao1.......................................................................... 73, 74

Docker イメージ....................................................... 20, 116

Feature table の集計......................................................63

CheckM................................................................. 136, 159

Docker - インストール...................................................... 15

fecal microbiota transplantation..........................172

classify-sklearn コマンド（qiime）...............................65

Docker - リソースの割り当て.......................................... 16

FGB.....................................................................................139

clr .........................................................................................78

DOI.................................................................................... 200

figshare............................................................................ 202

Clusters of Orthologous Groups..........................153

DOI と URL の関係......................................................... 201

figshare - 公開済みのデータのバージョンアップ....... 209

co-assembly.................................................................. 138

Domain...............................................................................66

figshare - コレクション機能......................................... 208

COG...................................................................................153

DRA..........................................................................182, 213

figshare - データ共有.................................................... 202

collapse コマンド（qiime）......................................67, 77

DRA XML 生成プログラム............................................ 184

Figtree...............................................................................142

Common Workflow Language（ワークフロー言語）

DRA データの公開...........................................................191

filter-features-conditionally コマンド（qiime）......69..........................................................................................23

DRA メタデータ............................................................... 185

filter-samples コマンド（qiime）...................................77

Completeness...............................................................159

dRep.................................................................................. 138

filter-table コマンド（qiime）......................................... 81

CONCOCT..................................................................... 136

dysbiosis..........................................................................173

conda install コマンド..................................................126

FMT....................................................................................172
for 文..................................................................................... 61

conda create コマンド..................................................126
conda env create コマンド...........................................46EG

conda update conda コマンド...................................45

EBI Sequence Read Archive....................................213

conda - アップデート........................................................45

eggNOG-mapper.............................................. 153, 165

Galaxy............................................................................... 111

conda コマンド........................................................ 19, 126

Elastic IP アドレス.............................................................40

Galaxy コンテナ...............................................................116

Contamination..............................................................159

EMP......................................................................................59

GCA....................................................................................161

core-metrics-phylogenetic コマンド（qiime）.......72

ENA................................................................................... 158

GCF....................................................................................161

csvcut コマンド..................................................................50

ennaf コマンド................................................................. 107

GCP......................................................................................24

csvkit - インストール.........................................................48

ENV....................................................................................192

GenBank......................................................................... 158

curl - インストール........................................................... 100

Environmental/Metagenome Genomic

GenBank 形式.................................................................155

curl コマンド...........................................................101, 155

Sequences. ............................................... 186

Genome Search Toolkit............................................102

Cutadapt..................................................................89, 128

ERA.....................................................................................213

Genome Taxonomy DataBase.............................. 140

CWL（ワークフロー言語）.................................................23

Experiment.................................................................... 185

Genome Taxonomy Database.............................. 169

export2graphlan..........................................................143

GenomeSync データベース............................................99

export コマンド（qiime）.................................................82

Genomics Standards Consortium....................... 186

D
DADA2........................................................................58, 86

INDEX

C

genus-level genome bins..........................................139
getentry........................................................................... 195

231

GFF/GTF 形式.................................................................155

known species-level genome bin........................ 140

Microsoft Azure..............................................................24

GGB....................................................................................139

KO.......................................................................................153

MIMAG............................................................................ 148

gneiss..................................................................................77

KOALA ウェブサービス.................................................. 168

MIMAG パッケージ........................................................ 186

Google Cloud Platform...............................................24

Kraken 2.................................................................106, 118

MIMS パッケージ............................................................. 186

GraPhlAn................................................................124, 142

Krona.................................................................................112

Miniconda......................................................................... 14

GraPhlAn - アノテーションファイル.............................143

Krona chart.......................................................... 102, 105

Miniconda - インストール............................................... 14graphlan_annotate.py.................................... 143, 144

kSGB................................................................................. 140

MiniKraken 2..................................................................113

Greengenes............................................................ 48, 113

Kyoto Encyclopedia of Genes and Genomes

minimap2.........................................................................102

grep コマンド...................................................................... 51........................................................................................153

MIxS パッケージ.............................................................. 186

GSC.......................................................................... 148, 186

mNGS..................................................................................98

GSTK..................................................................................102

L

mOTUs..............................................................................139

GTDB...................................................................... 140, 169

Latent Environment Allocation............................. 228

MyCC................................................................................ 136

GTDB-Tk................................................................ 140, 169

LEA.............................................................................. 87, 228

gunzip コマンド................................................................155

libtbb2............................................................................. 134

gstk.pl............................................................................... 103

multi-FASTA....................................................................191

N

Lifelines-DEEP............................................................... 177
Location........................................................................... 194

NAF................................................................................... 100

M

NCBI Assembly.....................................................99, 154

Homebrew......................................................................101

MAG...............................................................131, 152, 183

NCBI Sequence Read Archive................................213

HUMAnN.........................................................................170

MAG - アノテーション.................................................... 154

NCBI Taxonomy....................................................99, 183

MAG - 登録............................................................ 182, 185

Nextflow（ワークフロー言語）.......................................23

I

makeblastdb コマンド..................................................162

NGS データの登録...........................................................182

IAM ユーザー.......................................................................25

Maxbin2................................................................ 134, 135

IBD......................................................................................173

Median frequency.........................................................64

H

NanoGalaxy................................................................... 111

head コマンド.....................................................................50
heatmap コマンド（qiime）............................................70

NCBI BioSample.......................................................... 183

MAPLE.............................................................................. 169

Oimport コマンド（qiime）................................................54

MEGA................................................................................142

ONT......................................................................................98

INSD...................................................................................182

Megahit........................................................................... 130

ONT -- Metagenomics-Kraken2-Krona..............112

IP アドレス............................................................................32

MEO...................................................................................217

OPERA-MS.......................................................................131

iTOL v5..............................................................................143

MetaBAT1....................................................................... 134

Operational Taxonomic Unit....................................57

MetaBAT2....................................................................... 134

OTU......................................................................................57

metaFlye..........................................................................131

OTU 配列...........................................................................139

Metagene Annotator...................................... 153, 160

Oxford Nanopore Technologies.............................98

J
Japanese Genotype-phenotype Archive........ 196
JGA.................................................................................... 196

Metagenome-Assembled Genome....................................................................131, 152, 183

Pmetagenomic Next-Generation Sequencing....98K

metagenomic operational taxonomic units....139
MetaLAFFA.....................................................................170

PERMANOVA 検定..........................................................76

KBase.................................................................................170

MetaPlatanus.................................................................131

Permutational multivariate analysis of variance

KEGG.................................................................................153

MetaQuast......................................................................133..........................................................................................76

KEGG Orthology..........................................................219

metaSPAdes...................................................................131

PGAP..................................................................................161

KEGG pathway..............................................................219

MGnify................................................................................86

Phenotype.......................................................................215

KEGG-Decoder........................................ 153, 165, 168

MicrobeDB.jp.........................................................87, 211

phylophlan......................................................................139

KneadData......................................................................128

Microbes/Metagenomes Environmental

kneaddata_database コマンド.................................128232

メタゲノムデータ解析

Ontology.....................................................................217

PCoA......................................................................... 75, 226

phylophlan_metagenomic コマンド......................139
phylophlan_write_config_file コマンド.................141

16Sも! ショットガンも! ロングリードも! 菌叢解析が得意になる凄技レシピ

PhyloPhlAn3.........................................................124, 139

scp コマンド..................................................................... 188

phylophlan コマンド......................................................142

Secure Shell......................................................................32

Phylum................................................................................66

sendsketch コマンド......................................................129

V3 ～ 4 領域........................................................................59

pigz コマンド.......................................................................52

seqkit コマンド......................................................132, 133

V4 領域......................................................................... 48, 59

pigz コマンド - インストール.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

seq コマンド（seqkit）..........................................132, 133

Value................................................................................. 194

pip コマンド...................................................................... 165

SFTP.................................................................................. 188

virome...............................................................................149

PK ／ PD 解析...................................................................176

SGB.....................................................................................139

Virtual Private Cloud....................................................29

Prodigal....................................................... 136, 153, 160

Shannon...................................................................74, 227

VITCOMIC2.................................................... 86, 87, 228

Project 10K.................................................................... 177

Silva............................................................................ 48, 113

VPC.......................................................................................29

PROKKA........................................................................... 140

SILVAngs.............................................................................86

Python................................................................................. 14

SPAdes..............................................................................131
Species-level Genome Bin.......................................139

V

W
Weighted Unifrac 距離.................................................75
wget - インストール.........................................18, 46, 100

QC フィルター.....................................................................60

SSH........................................................................................32

workflow-meetup（ワークフロー言語の研究会）.....23

QIIME 2.......................................................................44, 86

stats コマンド（seqkit）.................................................132

WSL 1..................................................................................22

QIIME 2 artifacts............................................................84

submission-excel2xml.............................................. 188

WSL 2........................................................................13, 148

QIIME 2 View...................................................................55

subsample-paired コマンド（qiime）.........................58

W 値......................................................................................78

QIIME 2 - Docker イメージ............................................ 21

summarize コマンド（qiime）........................................55

QIIME 2 - インストール............................................ 19, 46

Supplemental Data.................................................... 202

qiime tools import コマンド........................................83

SVG 形式の画像................................................................. 81

qiime2R...............................................................................84
Qualifier.......................................................................... 194
Quality Score...................................................................56

INDEX

SRA............................................................................. 49, 213
SRA-Tools - インストール................................................47

Q

X
xargs コマンド.................................................................... 51

T

qza のデータファイル................................................55, 84

tabulate コマンド（qiime）.............................................68

qzv の可視化用のファイル.................................................55

tar.gz 圧縮...........................................................................96

Y
YAML ファイル.................................................................... 19

taxonomy_krona_chart.............................................118

R

text_processing............................................................118

RAxML...............................................................................141

The Genomic Standards Consortium................ 148

アクセッション番号................................................ 192, 195

rCDI....................................................................................173

Trimmomatic..................................................................128

アセンブリ................................................................129, 152

The Earth Microbiome Project................................59

RDP..............................................................................87, 113
re-assembly....................................................................137
relative-frequency コマンド（qiime）.........................67

あアセンブリグラフ...............................................................132

U

アトピー性皮膚炎............................................................. 224
アノテーション..................................... 140, 152, 154, 165

rename - インストール.....................................................47

Ubuntu........................................................................ 13, 27

アノテーションファイルの作成.........................................191

rename コマンド...............................................................52

UC.......................................................................................173

アノテーションリスト........................................................ 201

representative ゲノム配列........................................... 107

UME.................................................................................. 184

α - レアファクションカーブ...............................................71

Ribosomal Database Project....................................87

UniFrac 距離......................................................................75

α多様性...............................................................................71

rimAI..................................................................................141

UniRef90..........................................................................153

α多様性解析.......................................................................72

rRNA 遺伝子.................................................................... 156

UniRef90 のダウンロード..............................................161

アンプリコン解析...................................................... 86, 113

Run..................................................................................... 185

UNIX シェル........................................................................ 13

アンプリコンシークエンス.................................................44

unknown specieslevel genome bin.................... 140

Sunnaf コマンド................................................................. 106
uSGB................................................................................. 140

いSampling depth...............................................................64

遺伝子存在量.....................................................................170

samtools faidx コマンド...............................................132

医薬品.................................................................................172233

インスタンス - 開始.............................................................39

仮想環境を呼び出す（conda）.........................................47

系統組成と環境の関連性............................................87, 94

インスタンス - 起動.............................................................26

仮想マシンを作成................................................................25

系統組成の距離...................................................................94

インスタンス - 作成..................................................... 25, 33

がん........................................................................... 173, 224

系統組成の視覚化（門レベル）..........................................91

インスタンス - 詳細の設定.................................................29

環境情報...............................................................................87

系統組成の推定...................................................................89

インスタンス - 接続.............................................................34

環境と系統組成の関連性............................................87, 94

系統組成（門レベル）..........................................................91

インスタンス - タイプの選択.............................................28

環境トピック組成................................................................94

系統組成を調べる.............................................................217

インスタンス - タイプを変更.............................................37

環境名で検索.....................................................................217

系統的な距離.......................................................................91

インスタンス - 停止......................................................37, 40

環状ゲノム...........................................................................192

系統分類...............................................................................65

インストール（Anaconda/Docker）............................. 10

関連解析....................................................................... 73, 75

ゲノムアノテーション..........................................................152

インストールに失敗.............................................................22

ゲノム（系統）......................................................................211

きう

ゲノムの完成度...................................................................155
健康介入.............................................................................175

キーペア....................................................................... 32, 33

検出限界の検証...................................................................80

ウェブサービス...................................................................110

キーワード検索..................................................................211

建築環境.............................................................................219

ウェブツール.........................................................................86

擬似検体............................................................................ 103

運動.....................................................................................172

擬似的な細菌群集...............................................................88

こ

希釈化曲線...........................................................................71

え

基準株................................................................................ 158

公開鍵...................................................................................32

希少種................................................................................... 74

抗生物質投与.................................................................... 224

エラーの対処法....................................................................22

機能アノテーション..................................................152, 167

構造アノテーション............................................................152

エラーメッセージ..................................................................80

機能組成.............................................................................219

国際塩基配列データベース..............................................182

炎症性腸疾患.....................................................................173

キメラ配列除去後................................................................60

国立遺伝学研究所生命情報・DDBJ センター.............182

エントリ..............................................................................191

共アセンブル..................................................................... 138

コンセンサス配列..............................................................131

共著者................................................................................ 205

コンタミネーション.................................. 79, 95, 101, 155

お

距離.................................................................................... 227

コンティグ...........................................................................131

菌移植.................................................................................172

コントロールサンプル..........................................................80

オーバーラップ.....................................................................59

菌カクテル製剤..................................................................173

オフィスビル.......................................................................219

菌群設計.............................................................................176

オルソロガス遺伝子...................................... 136, 140, 153

菌種組成.......................................................................44, 65

オルソログ（遺伝子）.........................................................211

菌叢距離...............................................................................75

再発性 Clistridum difficile 感染症.............................173

菌叢構造...............................................................................76

査読者................................................................................ 205
サプリメント.......................................................................174

かくサンプリング深度........................................................ 64, 71

解析環境...............................................................................24

クオリティ低下.....................................................................56

サンプル数............................................................................56

解析サーバー........................................................................24

クオリティの悪いデータ.....................................................83

サンプル分離源................................................................. 183

階層クラスタリング.......................................................... 227

クラウドコンピューティングサービス...............................24

界 .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . 66

解像度.................................................................................132

クラスタリング...........................................................57, 227

潰瘍性大腸炎.....................................................................173

クリーニング.......................................................................127

サンプリングバイアス.......................................................139

し可視化（LEA）......................................................................87

シークエンスデータの入手.................................................49

可視化用のファイルに変換（QIIME 2）..........................55

けシークエンス（複数回のラン）............................................82

仮想環境（conda）................................................ 126, 140

系統解析.....................................................................65, 124

シェルスクリプト.................................................................23

仮想環境を activate（conda）.......................................20

系統樹の作成...........................................................124, 142

シェルプロンプト.................................................................45

仮想環境を deactivate（conda）..................................20

系統推定.............................................................................141

自己免疫疾患.....................................................................173

仮想環境を作成（conda）................................................. 19

系統組成.............................................................................114

疾患名オントロジー......................................................... 224

仮想環境............................................................................... 10234

さ

メタゲノムデータ解析

シークエンスプラットフォーム.........................................192

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実行環境を呼び出す...........................................................54

属より上位の生物分類..................................................... 184

室内環境.............................................................................217

属レベルの分類......................................................106, 184

特定の分類群をフィルター................................................. 81

宿主.....................................................................................211

存在量...................................................................................91

都市空間のメタゲノム........................................................129

宿主の進化系統................................................................ 224
宿主リードのフィルタリング............................................128
主座標分析...........................................................................75

登録日................................................................................ 221

土壌.................................................................................... 221

たトピックモデル.....................................................................87
ドラフトゲノム（WGS）を登録...................................... 196

種組成の解析.....................................................................124

ターミナル............................................................................. 12

トランスクリプトームデータ.............................................175

種名の同定........................................................................ 158

大学キャンパス..................................................................219

トリミング長.........................................................................59

種レベルの分類................................................................ 106

代謝性疾患.........................................................................173

消化器疾患.........................................................................173

代謝パスウェイ................................................................. 168

冗長な領域........................................................................ 156

体内動態.............................................................................176

食事.....................................................................................172

代表配列の可視化...............................................................63

ナノポアシークエンサー...................................................110

な多様性...................................................................................44

生データファイルのアップロード................................... 188

多様性指数........................................................................ 227

生データファイルの検証.................................................. 190

ショットガンシークエンス........................................98, 124

多様性指数の検定............................................................... 74

難培養微生物種.................................................................152

ショットガンメタゲノム解析................................................86

単独菌製剤.........................................................................173

真菌叢（ITS 領域）のデータ.............................................84

単離環境.............................................................................211

シングルコピーオルソロガス遺伝子..................... 136, 140

単離環境の pH................................................................. 224

シングルコピーマーカー遺伝子....................................... 136

単離環境の温度................................................................ 224

ネガティブコントロール......................................................79

単離環境名で検索.............................................................217

年齢.................................................................................... 224

診断.....................................................................................172

INDEX

食事指導.............................................................................176
食品.....................................................................................174ね

単離場所............................................................................ 221

す
水中.....................................................................................216

ちはパーキンソン病...................................................................173

睡眠.....................................................................................172

地域.................................................................................... 221

パイチャート.............................................................105, 114

スケーリング.........................................................................24

知財.....................................................................................173

パイプ.................................................................................... 51

ストレージの設定................................................................30

チャイム................................................................................44

配列が分断........................................................................ 156

スリープしない設定............................................................. 11

中間データ........................................................................ 199

配列類似性検索...................................................................87

注釈付き系統樹の作成...........................................124, 142

せ中枢疾患.............................................................................173
腸内細菌叢.........................................................................173

ひ精神疾患.............................................................................173

腸内細菌叢解析................................................................ 106

ヒートマップ..................................................... 69, 168, 226

精度検証...............................................................................79

治療.....................................................................................172

比較解析............................................................................ 221

生物種の比率.................................................................... 105
生物種名の同定................................................................ 158

微生物名で検索.................................................................215て

ヒトゲノム............................................................................101

セキュリティグループの設定（AWS）...............................32

ディファレンシャルカバレッジビンニング法................. 134

ビニング..............................................................................133

セキュリティ対策（AWS）..................................................25

データ解析環境................................................................... 10

皮膚疾患.............................................................................173

喘息.................................................................................... 224

データ共有........................................................................ 200

肥満.....................................................................................176

占有率............................................................................67, 68

データベース.......................................................................211

秘密鍵...................................................................................32

鉄道.....................................................................................219

表現型.................................................................................215とふ

創薬.....................................................................................172

統計的潜在意味解析..........................................................87

フィルタリング...................................................................128

属組成........................................................................... 86, 92

糖尿病.................................................................................173

不完全なビン.................................................................... 136

生命科学系データベースアーカイブ.................... 201, 207

そ相同性検索...........................................................................82

ヒトメタゲノムデータ........................................................ 196

235

服薬.....................................................................................172
プライマー配列....................................................................59

めりプライマリーメタゲノム.................................................... 196

メガビン............................................................................. 136

リード数................................................................................56

プログラムのバージョン.....................................................22

メタ 16S 解析.......................................................................44

リード長................................................................................56

プロビジョニング................................................................ 41

メタゲノムアセンブリ.....................................124, 129, 152

リードのクリーニング.......................................................127
リードのサンプリング.........................................................58

分子系統樹...........................................................................71

メタゲノムアセンブリ - データ区分.................................182

糞便移植療法.....................................................................172

メタゲノムアセンブリ - 登録先.........................................182

リダイレクト......................................................................... 51

糞便精製剤.........................................................................173

メタゲノムアセンブリデータの登録................................ 184

臨床データ.........................................................................176

分類階級の検索.................................................................115

メタゲノム（環境）...............................................................211

分類階層...............................................................................67

メタゲノムコンティグのアノテーション........................... 165

分類学的階級.......................................................................66

メタゲノム名....................................................................... 183

分類学的構造とメタデータの関連付け..........................124

メタゲノムデータ..................................................................98

分類群のアサイン..............................................................139

メタデータ................................................................201, 211

分類群レベル.................................................................... 226

メタデータと分類学的構造の関連付け..........................124

る
類似環境............................................................................ 220

れメタデータの作成......................................................53, 188
メタデータのダウンロード.................................................49

へ

レポジトリ............................................................................86

メタトランスクリプトーム解析...........................................96

ペアエンドリード.................................................................60

メタトランスクリプトームデータ........................................98

β多様性................................................................................71

メタボリック症候群...........................................................173

β多様性解析.......................................................................75

メタボロームデータ...........................................................176

ペットのゲノム....................................................................129

免疫.....................................................................................176ろロングリードシークエンス........................................98, 131

ヘルスケア..........................................................................172
変動菌種の検出...................................................................77

もほ

模擬コミュニティ.................................................................68

わ
ワークフロー......................................................................112
ワークフロー言語................................................................23

モダリティ..........................................................................172

棒グラフ................................................................................66

Bioconda コミュニティ..................................................126

ポジティブコントロール..............................................68, 79

モックコミュニティ.............................................................88
門 ..........................................................................................66

まマーカー遺伝子................................................................. 138

ゆマージ....................................................................................60

有心対数比変換...................................................................78

マイクロバイオーム関連治療薬.......................................173

優占系統...............................................................................95

マイクロバイオームデータ........................................86, 211

ユニバーサルプライマー.....................................................48

前処理...................................................................................89
マッピング..........................................................................170
マッピング精度................................................................. 106

よ葉緑体................................................................................... 81
予防.....................................................................................172

み予防療法.............................................................................175

ミトコンドリア...................................................................... 81
未培養の微生物.................................................................159
民族性................................................................................ 224

らライブラリ............................................................................ 14236

メタゲノムデータ解析

16Sも! ショットガンも! ロングリードも! 菌叢解析が得意になる凄技レシピ