{"id":1835,"date":"2023-05-04T17:43:21","date_gmt":"2023-05-04T08:43:21","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=1835"},"modified":"2026-04-15T15:56:52","modified_gmt":"2026-04-15T06:56:52","slug":"tutorial-microbiome-analysis-amplicon-sequencing","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/tutorial-microbiome-analysis-amplicon-sequencing\/","title":{"rendered":"Tutorial &#8211; Microbiome Analysis (amplicon sequencing)"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Introduction<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Microbimoe\uc740 \ud658\uacbd \uc548\uc5d0 \uc874\uc7ac\ud558\ub294 \ubbf8\uc0dd\ubb3c \uc804\uccb4\ub97c \uc758\ubbf8\ud55c\ub2e4. \ubbf8\uc0dd\ubb3c \uac04 \uc0c1\ud638\uc791\uc6a9 \ubc0f \ubbf8\uc0dd\ubb3c\uacfc \ud658\uacbd\uc758 \uc0c1\ud638\uc791\uc6a9 \uc5f0\uad6c\ub97c \ud1b5\ud574, microbiome\uc758 \uae30\ub2a5\uc744 \uc5f0\uad6c\ud560 \uc218 \uc788\ub2e4. \ud2b9\ud788 \uc0ac\ub78c\uc758 \uc7a5 \ud639\uc740 \ud53c\ubd80 \ub4f1\uc5d0 \uc11c\uc2dd\ud558\ub294 \ubbf8\uc0dd\ubb3c\uc774 \uc778\uccb4\uc758 \uac74\uac15\uacfc \uc9c8\ubcd1\uc5d0 \ubbf8\uce58\ub294 \uc601\ud5a5\uc774 \ud65c\ubc1c\ud558\uac8c \uc5f0\uad6c\ub418\uace0 \uc788\ub2e4. \uc774\ub7ec\ud55c \uc5f0\uad6c\ub97c \uc704\ud574\uc11c\ub294 \ubbf8\uc0dd\ubb3c\uc5d0 \ub300\ud55c \ub370\uc774\ud130\ub97c \ud68d\ub4dd\ud574\uc57c \ud558\ub294\ub370, \ub450 \uac00\uc9c0 NGS \uc2e4\ud5d8 \ubc29\ubc95\uc774 \ub110\ub9ac \uc774\uc6a9\ub41c\ub2e4. <strong>Amplicon sequencing<\/strong>\uc740  \ud2b9\uc815 \uc11c\uc5f4\uc744 \uac00\uc9c4 DNA\ub97c PCR\uc744 \uc774\uc6a9\ud574 \uc99d\ud3ed\ud55c \ub4a4 \uc11c\uc5f4\uc744 \uacb0\uc815\ud558\ub294 \uc2e4\ud5d8 \ubc29\ubc95\uc73c\ub85c, \uc138\uade0\uc744 \ub300\uc0c1\uc73c\ub85c \ud560 \ub54c\ub294 \uc138\uade0\uc758 ribosome\uc744 \ucf54\ub529\ud558\ub294 \uc720\uc804\uc790\uc778 16S rRNA \uc11c\uc5f4\uc744 \uc99d\ud3ed\ud558\uc5ec \ubd84\uc11d\ud55c\ub2e4. <strong>Whole metagenome sequencing<\/strong>\uc740 \uc0d8\ud50c(\ud639\uc740 \ud658\uacbd)\uc548\uc5d0 \uc788\ub294 DNA\ub97c \uc870\uac01\ub0b8 \ud6c4 \uadf8 \uc11c\uc5f4\uc744 \uacb0\uc815\ud558\ub294 \ubc29\ubc95\uc73c\ub85c \ud2b9\uc815\ud55c \ud658\uacbd\uc5d0 \uc788\ub294 \uc138\uade0\uc774 \uac00\uc9c4 DNA \uc11c\uc5f4\uc744 \ud1b5\ud574 \uc720\uc804\uc790\uc758 \uc885\ub958\uc640 \uc591\uc744 \ubd84\uc11d\ud558\uc5ec, \ud2b9\uc815\ud55c \ubd84\uc790\uc801 \uae30\ub2a5\uc758 \ud65c\uc131\ud654\/\uc800\ud558\ub97c \ubd84\uc11d\ud558\ub294 \ubc29\ubc95\uc774\ub2e4.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Prerequisite<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Tutorial  \uc9c4\ud589\uc5d0 \uc55e\uc11c \uc544\ub798\uc758 \ub0b4\uc6a9\uc744 \uc219\uc9c0\ud55c\ub2e4.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/microbiome-in-health-and-disease\/\">Microbiome in health and disease<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/next-generation-sequencing-ngs\/\">Next generation sequencing<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/amplicon-sequencing\/\">Amplicon sequencing<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/anaconda\/\">Anaconda<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Summary<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Tutorial \uc804\uccb4 \uacfc\uc815 \uac04\ub2e8 \uc694\uc57d<\/p>\n\n\n\n<div class=\"inherit-container-width wp-block-group has-ast-global-color-4-background-color has-background is-layout-constrained wp-block-group-is-layout-constrained\">\n<ul class=\"wp-block-list\">\n<li>Input: amplicon sequencing data (FASTQ format file, paired end sequencing)<\/li>\n\n\n\n<li>Intermediate data\n<ul class=\"wp-block-list\">\n<li>Representative sequences (sequence of unique amplicons)<\/li>\n\n\n\n<li>Feature table (microbial profile of individuals)<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Output\n<ul class=\"wp-block-list\">\n<li>Taxonomic profile<\/li>\n\n\n\n<li>Functional profile<\/li>\n\n\n\n<li>Host factor association<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"434\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/07\/summary-1024x434.png\" alt=\"\" class=\"wp-image-2233\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/07\/summary-1024x434.png 1024w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/07\/summary-300x127.png 300w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/07\/summary-768x326.png 768w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/07\/summary-1536x651.png 1536w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/07\/summary-2048x868.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Tutorial<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Summary<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>(\ubaa9\uc801)<\/strong> Amplicon sequencing \uc2e4\ud5d8 \uacb0\uacfc \uc5bb\uc5b4\uc9c4 FASTQ format \ub370\uc774\ud130\ub97c \uc774\uc6a9\ud558\uc5ec \ubbf8\uc0dd\ubb3c\uc758 profile\uc744 \uad6c\ud558\uace0, \uae30\ucd08\uc801\uc778 \ubd84\uc11d \ubc29\ubc95\uc758 \uc885\ub958\ub97c \uc774\ud574\ud55c\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>(\ubc29\ubc95)<\/strong> QIIME2 suite\ub97c \uc774\uc6a9\ud558\uc5ec \uc0d8\ud50c \ubcc4 FASTQ format \ud615\ud0dc\ub85c \uc815\ub9ac\ub41c amplicon sequencing \ub370\uc774\ud130\ub97c \uc0d8\ud50c\uc5d0 \uc874\uc7ac\ud558\ub294 <strong>(1) DNA \uc11c\uc5f4<\/strong>\uacfc <strong>(2) \uc0d8\ud50c \ubcc4 \ud574\ub2f9 DNA \uc11c\uc5f4\uc758 \uac1c\uc218\ub85c \uad6c\uc131\ub41c \ud45c<\/strong>\ub85c \ubcc0\ud658\ud558\uace0, \uc774\ub807\uac8c \ubcc0\ud658\ub41c \uc815\ubcf4\ub97c \uc774\uc6a9\ud574 \ub2e4\uc591\uc131 \ubd84\uc11d\uc744 \uc218\ud589\ud55c\ub2e4. \uc5ec\uae30\uc11c DNA \uc11c\uc5f4\uc740 <strong>representative sequence<\/strong> , \uc0d8\ud50c \ubcc4 DNA \uc11c\uc5f4 \uac1c\uc218\ud45c\ub294 <strong>feature table<\/strong>\uc774\ub77c \ud55c\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>(\ucd94\uac00)<\/strong> \uc774 tutorial\uc740 amplicon sequencing \uc2e4\ud5d8 \ub370\uc774\ud130 \ubd84\uc11d\uc758 \uc804\uc0b0\uc801 \uacfc\uc815\uc744 \ud45c\ud604\ud55c \uac83\uc73c\ub85c, \uac01\uac01\uc758 \ub2e8\uacc4\uc5d0 \ub300\ud55c \uc790\uc138\ud55c \ub0b4\uc6a9\uc744 \ud559\uc2b5 \ubc0f \uc774\ud574\uac00 \ud544\uc694\ud558\ub2e4. \ub610\ud55c \uc774 tutorial\uc740 \uae30\ubcf8\uc801\uc778 \ubd84\uc11d \uacfc\uc815 \ub9cc\uc744 \ud3ec\ud568\ud558\uace0 \uc788\uc73c\ubbc0\ub85c, \ub2e4\uc591\ud55c \uc751\uc6a9 \uc5f0\uad6c\ub97c \uc704\ud574\uc11c\ub294 \ud1b5\uacc4\uc801\uc778 \ubc29\ubc95\ub860 \ubc0f \uae30\uacc4\ud559\uc2b5 \ubc29\ubc95\ub860\uc744 \ud559\uc2b5\ud558\uc5ec \uc801\uc6a9\ud560 \ud544\uc694\uac00 \uc788\ub2e4. <\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Tutorial \uac01 \uacfc\uc815\uc758 \uc774\ub860\uc801 \ubc30\uacbd \ud559\uc2b5<\/li>\n\n\n\n<li>Feature table- \uac74\uac15 \uc9c0\ud45c \uc0c1\ud638 \uad00\ub828\uc131 \ubd84\uc11d <\/li>\n\n\n\n<li>Feature table \uc774\uc6a9 \uac74\uac15 \uc9c0\ud45c \uc608\uce21<\/li>\n\n\n\n<li>Representative sequence \uc11c\uc5f4 \uae30\ubc18 feature \ubcc0\ud658 (functionality analysis, like picrust2)<\/li>\n<\/ol>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>(\uc0ac\uc804\uc9c8\ubb38)<\/strong> Tutorial \uc9c4\ud589\uc5d0 \uc55e\uc11c \uc544\ub798\uc758 \uc9c8\ubb38\uc5d0 \ub2f5\ud574\ubcf4\uace0, \uc544\ub798 \uc9c8\ubb38\uc5d0 \ub2f5\ud558\uae30 \uc5b4\ub824\uc6b0\uba74 prerequisite\uc758 \uc8fc\uc81c\ub4e4\uc744 \ub2e4\uc2dc \ud55c\ubc88 \uc0b4\ud3b4\ubcf8\ub2e4.<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>FASTQ format \ud30c\uc77c\uc740 \ubb34\uc5c7\uc778\uac00?<\/li>\n\n\n\n<li>16S rRNA sequencing\uc744 \ud1b5\ud574 \uc5bb\uc740 FASTQ \ud30c\uc77c\uc740 \uc5b4\ub5a4 \uc815\ubcf4\ub97c \uac00\uc9c0\uace0 \uc788\ub294\uac00? <\/li>\n\n\n\n<li>Forward read\uc640 reverse read\ub294 \ubb34\uc5c7\uc778\uac00? <\/li>\n\n\n\n<li>V3-V4 region\uc774\ub780 \ubb34\uc5c7\uc778\uac00?<\/li>\n<\/ol>\n\n\n\n<h3 class=\"wp-block-heading\">1. Tutorial \ud30c\uc77c \ubc1b\uae30<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Tutorial \uc2e4\ud589\uc744 \uc704\ud574 Visual Studio Code (VSC)\ub97c \uc774\uc6a9\ud574 \uc11c\ubc84\uc5d0 \uc811\uc18d\ud558\uace0, \uc791\uc5c5 \ub514\ub809\ud1a0\ub9ac\ub97c \uc0dd\uc131\ud558\uace0, \ud544\uc694\ud55c \ud30c\uc77c\uc744 \ub2e4\uc6b4 \ubc1b\ub294\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>1.1. \uc791\uc5c5 directory \ub9cc\ub4e4\uae30<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\uc791\uc5c5 directory\ub97c \ub9cc\ub4e4\uace0 Visual Studio Code\uc5d0\uc11c \ud574\ub2f9 directory\ub97c \uc5f0\ub2e4. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">cd ~\nmkdir tutorial\ncd tutorial\nmkdir qiime2_amplicon<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>1.2. Tutorial \ud30c\uc77c \ubc1b\uae30<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\ud544\uc694\ud55c \ud30c\uc77c\uc744 \ub2e4\uc6b4 \ubc1b\ub294\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">cd ~\/tutorial\/qiime2_amplicon\nwget https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/05\/qiime2_tutorial.zip --no-check-certificate<\/code><\/pre>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-665967ac-c0cb-4eb2-9170-a66685d06493\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/05\/qiime2_tutorial.zip\">qiime2_tutorial<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/05\/qiime2_tutorial.zip\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-665967ac-c0cb-4eb2-9170-a66685d06493\">Download<\/a><\/div>\n\n\n\n<h3 class=\"wp-block-heading\">2. Install QIIME2<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">QIIME2 \ud504\ub85c\uadf8\ub7a8\uc744 \uc124\uce58\ud55c\ub2e4. \uc124\uce58\ub294 <strong>conda<\/strong>\ub97c \uc774\uc6a9\ud574\uc11c \uc9c4\ud589\ud55c\ub2e4. \uc544\ub798 \uba85\ub839\uc740 2022.2 \ubc84\uc804\uc758 QIIME2 suite \uc124\uce58\ub97c \uc704\ud55c \uc608\uc81c\uc774\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">QIIME2\ub294 microbiome \ubd84\uc11d\uc5d0\uc11c \uc790\uc8fc \uc0ac\uc6a9\ud558\ub294 \ud504\ub85c\uadf8\ub7a8\uc744 \ubaa8\uc544 \ub193\uc740 program suite\uc774\ub2e4. \ucd94\ud6c4 Web page\uc5d0\uc11c QIIME2\uc5d0 \ub300\ud55c \uc815\ubcf4\ub97c \ucd94\uac00\ub85c \uc218\uc9d1\ud558\ub3c4\ub85d \ud55c\ub2e4 (<a href=\"https:\/\/qiime2.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/qiime2.org\/<\/a>). <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\ud2b9\uc815 environment\uac00 \ud65c\uc131\ud654\ub418\uc5b4 \uc788\ub2e4\uba74, \uc544\ub798 \uba85\ub839\uc5b4\ub97c \uc774\uc6a9\ud574 \uba3c\uc800 \ubd88\ud65c\uc124\ud654 \uc2dc\ud0a4\uace0 \uc124\uce58\ub97c \uc9c4\ud589\ud55c\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">conda deactivate\nconda clean --all -y <\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">QIIME2 Environment \uc124\uce58 <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">conda env create -n qiime2-amplicon-2024.10 --file https:\/\/data.qiime2.org\/distro\/amplicon\/qiime2-amplicon-2024.10-py310-linux-conda.yml<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">3. Preprocess<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Microbiome \ubd84\uc11d\uc740 \uc5ec\ub7ec \uc0d8\ud50c\uc744 \ube44\uad50 \ubd84\uc11d\ud558\ub294 \uac83\uc774 \uc77c\ubc18\uc801\uc774\ub2e4. QIIME2\ub294 \ud769\uc5b4\uc838 \uc788\ub294 \uc5ec\ub7ec \ud30c\uc77c\uc744 \uc0c8\ub85c\uc6b4 \ud30c\uc77c \ud558\ub098\ub85c \ubaa8\uc740\ub2e4. \uc774 \uacfc\uc815\uc740 <code>qiime tools import<\/code> \ubc29\ubc95\uc744 \uc774\uc6a9\ud574 \uc9c4\ud589\ud55c\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>(FASTQ \ud30c\uc77c \uc774\ub984)<\/strong> \ubd84\uc11d\uc5d0 \ud65c\uc6a9\ub418\ub294 FASTQ \ud30c\uc77c\uc740 NGS \uae30\uae30\ub97c \ud1b5\ud574 \uc0dd\uc131\ub41c \uc6d0 \ub370\uc774\ud130\ub97c \uac00\uacf5\ud55c \uacb0\uacfc\ubb3c\uc774\ub2e4. Bar code \uc11c\uc5f4\uc744 \uc774\uc6a9\ud558\uc5ec \uc0d8\ud50c \ubcc4\ub85c \ubcc4\ub3c4\uc758 FASTQ \ud30c\uc77c\uc744 \uc0dd\uc131\ud558\ub294 \uac83\uc774 \uc77c\ubc18\uc801\uc774\ub2e4. \uc774 \uacfc\uc815\uc744 demultiplexing \uc774\ub77c \ud55c\ub2e4. \ub610\ud55c, paired sequencing\uc774 \uc77c\ubc18\uc801\uc778\ub370, \uc774 \ub54c \uc0dd\uc131\ub418\ub294 forward read\uc5d0\ub294 <code>_1<\/code>, reverse read\uc5d0\ub294 <code>_2<\/code>\uc640 \uac19\uc740 tag\ub97c \ubd99\uc5ec \ud45c\uae30\ud558\ub294 \uac83\uc774 \uc77c\ubc18\uc801\uc774\ub2e4.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>(Primer \uc11c\uc5f4)<\/strong> Primer \uc11c\uc5f4\uc740 PCR\uc744 \uc704\ud574 \ub3c4\uc785\ud55c \uc11c\uc5f4\uc774\uace0, redundancy\ub97c \uac00\uc9c4 \uc11c\uc5f4\uc744 \uc774\uc6a9\ud558\ub294 \uacbd\uc6b0\uac00 \ub9ce\uc774 \uc788\uae30 \ub54c\ubb38\uc5d0 \uc774\ub97c \uc81c\uac70\ud558\ub294 \uac83\uc774 \ubc14\ub78c\uc9c1\ud560 \uac83\uc774\ub2e4. \ub530\ub77c\uc11c \ucd94\uac00 \ubd84\uc11d\uc5d0 \uc55e\uc11c primer \uc11c\uc5f4 \uc81c\uac70\uac00 \ud544\uc694\ud558\ub2e4. <\/p>\n\n\n\n<h4 class=\"wp-block-heading\">3.1. QIIME2 \ud658\uacbd \ud65c\uc131\ud654<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">QIIME2 \uc2e4\ud589\uc744 \uc704\ud574\uc11c\ub294 \uc124\uce58\ud55c conda \ud658\uacbd\uc744 \ud65c\uc131\ud654 \uc2dc\ucf1c\uc57c \ud55c\ub2e4. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">conda activate qiime2-amplicon-2024.10 <\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">3.2. MANIFEST \ud30c\uc77c \ub9cc\ub4e4\uae30<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Manifest \ud30c\uc77c\uc740 \uc120\uc5b8 \ud30c\uc77c\uc774\ub77c\uace0\ub3c4 \ud558\uba70, \ud30c\uc77c\uc5d0 \ub300\ud55c \uc124\uba85\uc744 \ud3ec\ud568\ud558\ub294 \ud30c\uc77c\uc774\ub2e4. \ubd84\uc11d\uc5d0 \ud544\uc694\ud55c FASQT \ud30c\uc77c\uc758 \uc704\uce58\uc640 \uac01 \ud30c\uc77c\uc774 \ub300\uc751\ud558\ub294 \uc0d8\ud50c\uc5d0  \ub300\ud55c \uc815\ubcf4\ub97c \uc81c\uacf5\ud574\uc57c \ud55c\ub2e4. \uc774\ub97c \uc704\ud574 MANIFEST \ud30c\uc77c\uc744 \uc791\uc131\ud574\uc57c \ud55c\ub2e4. \uc774 \ud30c\uc77c\uc740 \uc0d8\ud50c identifier (<code>sample-id<\/code>), forward read \ud30c\uc77c \uc704\uce58 (<code>forward-absolute-filepath<\/code>), reverse read \ud30c\uc77c \uc704\uce58 (<code>forward-absolute-filepath<\/code>) \ub4f1\uc758 \uc815\ubcf4\ub97c \ud3ec\ud568\ud558\uba70, \uc544\ub798\uc640 \uac19\uc740 \ud30c\uc77c\uc744 \uc0dd\uc131\ud560 \uc218 \uc788\ub2e4. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"adoc\" class=\"language-adoc\">sample-id\tforward-absolute-filepath\treverse-absolute-filepath\nS001\t$PWD\/fastq\/ERR3472004_1.fastq\t$PWD\/fastq\/ERR3472004_2.fastq\nS002\t$PWD\/fastq\/ERR3472005_1.fastq\t$PWD\/fastq\/ERR3472005_2.fastq\nS003\t$PWD\/fastq\/ERR3472006_1.fastq\t$PWD\/fastq\/ERR3472006_2.fastq\nS004\t$PWD\/fastq\/ERR3472007_1.fastq\t$PWD\/fastq\/ERR3472007_2.fastq\nS005\t$PWD\/fastq\/ERR3472008_1.fastq\t$PWD\/fastq\/ERR3472008_2.fastq\nS006\t$PWD\/fastq\/ERR3472009_1.fastq\t$PWD\/fastq\/ERR3472009_2.fastq\nS007\t$PWD\/fastq\/ERR3472010_1.fastq\t$PWD\/fastq\/ERR3472010_2.fastq\nS008\t$PWD\/fastq\/ERR3472011_1.fastq\t$PWD\/fastq\/ERR3472011_2.fastq\nS009\t$PWD\/fastq\/ERR3472012_1.fastq\t$PWD\/fastq\/ERR3472012_2.fastq\nS010\t$PWD\/fastq\/ERR3472013_1.fastq\t$PWD\/fastq\/ERR3472013_2.fastq\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">(*) \uc774 \uc608\uc81c\uc5d0\uc11c <code>$PWD<\/code>\ub294 \ud604\uc7ac \ub514\ub809\ud1a0\ub9ac\ub97c \uc758\ubbf8\ud558\uba70, \ub2e4\ub978 \uc704\uce58\uc5d0 \ud30c\uc77c\uc774 \uc874\uc7ac\ud558\ub294 \uacbd\uc6b0 \ud574\ub2f9 \uc704\uce58\uc5d0 \ub300\ud55c \uc808\ub300 \uacbd\ub85c\ub97c \uc9c0\uc815\ud574\uc57c \ud55c\ub2e4.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">3.3. FASTQ \ud30c\uc77c \uc218\uc9d1<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">MANIFEST \ud30c\uc77c\uc5d0 \uae30\ub85d\ub418\uc5b4 \uc788\ub294 FASTQ \ud30c\uc77c\uc744 \uc218\uc9d1\ud558\uc5ec \ud558\ub098\uc758 \ud30c\uc77c(<code>paired-end-demux.qza<\/code>) \ud30c\uc77c\ub85c \ub9cc\ub4e0\ub2e4.<\/p>\n\n\n\n<pre title=\"1. preprocess.sh\" class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\"># Import FASTQ format files\nmkdir intermediate\nqiime tools import \\\n  --type 'SampleData[PairedEndSequencesWithQuality]' \\\n  --input-path manifest.tsv \\\n  --output-path intermediate\/paired-end-demux.qza \\\n  --input-format PairedEndFastqManifestPhred33V2 \n<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">3.4. PRIMER \uc11c\uc5f4 \uc81c\uac70<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Primer \uc11c\uc5f4\uc744 \uc81c\uac70\ud55c\ub2e4. (<code>paired-end-demux-trimmed.qza<\/code>)<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\"># Trim primer sequences\nqiime cutadapt trim-paired \\\n  --i-demultiplexed-sequences intermediate\/paired-end-demux.qza \\\n  --p-cores 20 \\\n  --p-front-f CCTACGGGNGGCWGCAG \\\n  --p-front-r GACTACHVGGGTATCTAATCC \\\n  --p-minimum-length 100 \\\n  --p-discard-untrimmed \\\n  --o-trimmed-sequences intermediate\/paired-end-demux-trimmed.qza\n<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">\ub2e8\uacc4 4. Denoising (DADA2)<\/h4>\n\n\n\n<h3 class=\"wp-block-heading\">4. Denoising and Amplicon Sequence Variant (ASV)  detection<\/h3>\n\n\n\n<h4 class=\"wp-block-heading\">4.1. Denoising (DADA2) and feature-table \ub9cc\ub4e4\uae30<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Amplicon sequencing\uc744 \ud1b5\ud574 \uc77d\uc740 sequence read\ub294 PCR \uacfc\uc815 \ubc0f sequencing \uacfc\uc815\uc758 error\ub97c \ud3ec\ud568\ud55c\ub2e4. \ub530\ub77c\uc11c, \ucd5c\uc885\uc801\uc73c\ub85c \uc77d\uc740 \uc11c\uc5f4\uc5d0 \uc624\ub958\uac00 \uc874\uc7ac\ud55c\ub2e4. \uc774 \uc624\ub958\ub97c \uc704\ud55c \ubc29\ubc95\uc73c\ub85c, \uc11c\uc5f4 \uc720\uc0ac\ub3c4\uc5d0 \uae30\ubc18\ud558\uc5ec \uc720\uc0ac \uc11c\uc5f4\uc744 \ubaa8\uc544 operational taxonomic unit (OTU)\ub97c \uad6c\uc131\ud558\ub294 \ubc29\ubc95\uc774 \ub110\ub9ac \uc774\uc6a9\ub418\uc5c8\ub2e4. \uad00\ub828 \ub0b4\uc6a9\uc744 \uc218\uc9d1\ud574\uc11c \uacf5\ubd80\ud558\ub3c4\ub85d \ud558\uc790. \ub2e4\ub978 \ubc29\ubc95\uc73c\ub85c \ud1b5\uacc4\uc801 \ubd84\uc11d\uc744 \ud1b5\ud574 \uc624\ub958\ub85c \uc778\ud574 \ubc1c\uc0dd\ud558\ub294 \uc11c\uc5f4\uc744 \ucc3e\uc544\uc11c \uc81c\uac70\ud560 \uc218 \uc788\ub2e4. \ub2e4\uc591\ud55c \ubc29\ubc95\uc774 \uc788\uc73c\ub098 \uadf8 \uc911 \ud558\ub098\uc778 DADA2\uac00 \ub110\ub9ac \ud65c\uc6a9\ub418\uace0 \uc788\ub2e4. \uc5ec\uae30\uc11c\ub294 \uc774 \ubc29\ubc95\uc744 \uc774\uc6a9\ud574 \uc11c\uc5f4\uc758 \uc624\ub958\ub97c \uc904\uc774\ub294 \ubc29\ubc95\uc744 \uc774\uc6a9\ud55c\ub2e4.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">QIIME2 DADA2 package\ub294 \ucd94\uac00\ub85c \uc77c\ub828\uc758 \ub370\uc774\ud130 \ucc98\ub9ac \uacfc\uc815\uc744 \uac70\uce58\uba70, \uc774\ub97c \ud1b5\ud574 \uace0\uc720\ud55c \uc11c\uc5f4\uc778 <strong>representative sequence(<code>representative_sequences.qza<\/code>)<\/strong> \uc640 \uc0d8\ud50c \ubcc4 read \uac1c\uc218\ub97c \ub098\ud0c0\ub0b4\ub294 \ud45c\uc778 <strong>feature-table (<code>table.qza<\/code>)<\/strong>\uc744 \uc0dd\uc131\ud55c\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\"># Generate feature table\nqiime dada2 denoise-paired \\\n  --i-demultiplexed-seqs intermediate\/paired-end-demux-trimmed.qza \\\n  --p-trunc-len-f 270 \\\n  --p-trunc-len-r 220 \\\n  --o-representative-sequences intermediate\/representative_sequences.qza \\\n  --p-n-threads 20 \\\n  --o-table intermediate\/table.qza \\\n  --output-dir .\/dada2_output\n<\/code><\/pre>\n\n\n\n<div class=\"inherit-container-width wp-block-group has-ast-global-color-6-background-color has-background is-layout-constrained wp-block-group-is-layout-constrained\">\n<p class=\"wp-block-paragraph\">DADA2 \ub17c\ubb38<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Callahan, B. J., et al. (2016). &#8220;DADA2: High-resolution sample inference from Illumina amplicon data.&#8221; Nat Methods 13(7): 581-583.<\/p>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-38a031b9-7e66-4538-bead-0a8a739aa349\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/05\/Callahan-2016-Dada-high-resolution-sample-inferen.pdf\">Callahan-2016-Dada-high-resolution-sample-inferen<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/05\/Callahan-2016-Dada-high-resolution-sample-inferen.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-38a031b9-7e66-4538-bead-0a8a739aa349\">Download<\/a><\/div>\n<\/div>\n\n\n\n<h4 class=\"wp-block-heading\">4.2. Rarefy <\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">\uac01 \uc0d8\ud50c \ubcc4\ub85c read \uc218\uc758 \ucc28\uc774\uac00 \ubc1c\uc0dd\ud55c\ub2e4. \uc774\ub7ec\ud55c \ucc28\uc774\ub294 \ucd94\ud6c4 \ubd84\uc11d \uacfc\uc815\uc5d0\uc11c \ubb38\uc81c\ub97c \uc77c\uc73c\ud0ac \uc218 \uc788\ub2e4. \ub530\ub77c\uc11c \uc0d8\ud50c \ubcc4 read \uc22b\uc790\ub97c \uac19\uac8c \ub9cc\ub4e4\uc5b4 \uc8fc\ub294 \uacfc\uc815\uc774 \ud544\uc694\ud558\ub2e4. \uc989, \uc0d8\ud50c\uc758 read \uac1c\uc218\ub97c 10,000\uac1c\ub85c \ud1b5\uc77c \uc2dc\ud0ac \uc218 \uc788\uc744 \uac83\uc774\ub2e4. \uc774 \uacbd\uc6b0 10,000\uac1c \uc774\ud558\uc758 read\ub97c \uac00\uc9c4 \uc0d8\ud50c\uc740 \uc0ad\uc81c\ub41c\ub2e4. \uc0d8\ud50c \ub2f9 read  \uac1c\uc218\uac00 \ub9ce\uc744 \uc218\ub85d \uc815\ubcf4 \uc591\uc740 \uc99d\uac00\ud558\uc9c0\ub9cc, \ubd84\uc11d\uc5d0 \uc0ac\uc6a9\ub418\ub294 \uc0d8\ud50c \uc22b\uc790\uac00 \uc904\uc5b4\ub4e4 \uc218\ub3c4 \uc788\ub2e4. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">\n# Rarefy\nqiime feature-table rarefy --i-table intermediate\/table.qza \\\n  --p-sampling-depth 10000 \\\n  --o-rarefied-table intermediate\/feature-table_rarefied.qza \\\n  --output-dir output_rarefaction<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">5. Microbiome analysis <\/h3>\n\n\n\n<h4 class=\"wp-block-heading\">5.1. Build phylogenetic trees<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">\uc11c\uc5f4 \uc720\uc0ac\ub3c4\uc5d0 \uae30\ubc18\ud558\uc5ec ASV \uac04 \uc720\uc0ac\ub3c4 \uce21\uc815\uc744 \uc704\ud55c \uacc4\ud1b5\uc218\ub97c \uc0dd\uc131\ud55c\ub2e4. \uc774 \uacc4\ud1b5\uc218\ub294 \ucd94\ud6c4 ASV \uc720\uc0ac\ub3c4 \ube44\uad50\uac00 \ud544\uc694\ud55c \ubd84\uc11d \uacfc\uc815\uc5d0 \ud65c\uc6a9\ud55c\ub2e4. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">qiime alignment mafft   --i-sequences intermediate\/representative_sequences.qza --o-alignment intermediate\/aligned.qza --p-n-threads 20\nqiime alignment mask --i-alignment intermediate\/aligned.qza --o-masked-alignment intermediate\/masked.qza\nqiime phylogeny fasttree --i-alignment intermediate\/masked.qza --o-tree intermediate\/unrooted-tree.qza --p-n-threads 20\nqiime phylogeny midpoint-root --i-tree intermediate\/unrooted-tree.qza --o-rooted-tree intermediate\/rooted-tree.qza\n<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">6. Diversity analysis<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Microbiome\uc740 \ubbf8\uc0dd\ubb3c\uc758 \uc0dd\ud0dc\uacc4\ub97c \uc5f0\uad6c\ud558\ub294 \uacfc\uc815\uc73c\ub85c \uc0dd\uac01\ud560 \uc218\ub3c4 \uc788\ub2e4. \ubbf8\uc0dd\ubb3c\uc758 \ub2e4\uc591\uc131\uc774 \ub192\uc744 \uc218\ub85d \ubcc0\ud654\ud558\ub294 \ud658\uacbd\uc5d0 \uc801\uc751\ud558\uae30 \uc26c\uc6b0\uba70, \ub2e4\uc591\ud55c \uc601\uc591\uc18c\ub97c \ub300\uc0ac \ud558\ub294 \ub4f1\uc758 \uae30\ub2a5\uc744 \uac00\uc9c8 \uc218 \uc788\ub2e4\uace0 \uc5ec\uaca8\uc9c4\ub2e4. \ub530\ub77c\uc11c \ubbf8\uc0dd\ubb3c \ub2e4\uc591\uc131 \ubd84\uc11d\uc774 \uac00\uc7a5 \uccab \ub2e8\uacc4\uc774\ub2e4. \ub2e4\uc591\uc131\ub3c4 \uc5ec\ub7ec \uac00\uc9c0 \uce21\uba74\uc5d0\uc11c \uace0\ub824\ud560 \uc218 \uc788\ub294\ub370, \uc77c\ubc18\uc801\uc73c\ub85c\ub294 \ud558\ub098\uc758 \ud658\uacbd\uc5d0\uc11c\uc758 \ub2e4\uc591\uc131\uacfc, \ub450 \ud658\uacbd\uc758 \ucc28\uc774\uc5d0\uc11c \uc624\ub294 \ub2e4\uc591\uc131 \ub450 \uac00\uc9c0\ub97c \ub9ce\uc774 \uace0\ub824\ud55c\ub2e4. \uc804\uc790\ub97c alpha diversity \ud6c4\uc790\ub97c beta diversity\ub77c \ud55c\ub2e4. <\/p>\n\n\n\n<h4 class=\"wp-block-heading\">6.1. Alpha diversity <\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Alpha diversity\ub294 \ud2b9\uc815 \ud658\uacbd \uc548\uc758 \ubbf8\uc0dd\ubb3c \ub2e4\uc591\uc131\uc744 \ub098\ud0c0\ub0b4\ub294 \uc9c0\ud45c\uc774\ub2e4. \uc7a5\ub0b4\ubbf8\uc0dd\ubb3c\ub85c \uc0dd\uac01\ud558\uba74, \ud55c \uc0ac\ub78c\uc758 \uc7a5\uc5d0 \uc5bc\ub9c8\ub098 \ub2e4\uc591\ud55c \ubbf8\uc0dd\ubb3c\uc774 \uc874\uc7ac\ud558\uace0 \uc788\ub294\uc9c0\uc5d0 \ub300\ud55c \uce21\uc815\uce58\ub77c\uace0 \ud560 \uc218 \uc788\ub2e4. \uc774\ub294 <code>diversity alpha<\/code> \ubaa8\ub4c8\uc744 \uc774\uc6a9\ud574 \uacc4\uc0b0\ud560 \uc218 \uc788\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\ub2e4\uc591\uc131\uc744 \uce21\uc815\ud558\ub294 \ubc29\ubc95\uc740 \uc5ec\ub7ec \uac00\uc9c0\uac00 \uc874\uc7ac\ud55c\ub2e4. \uc5ec\uae30\uc11c\ub294 Chao1, observed features, Shannon entropy\ub97c \uacc4\uc0b0\ud558\uc600\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\"># Create directories for analysis\nmkdir diversity\nmkdir results \n\n# alpha diversity\nqiime diversity alpha --i-table intermediate\/feature-table_rarefied.qza --p-metric chao1 --o-alpha-diversity diversity\/chao1_vector.qza\nqiime diversity alpha --i-table intermediate\/feature-table_rarefied.qza --p-metric observed_features --o-alpha-diversity diversity\/observed_features_vector.qza\nqiime diversity alpha --i-table intermediate\/feature-table_rarefied.qza --p-metric shannon --o-alpha-diversity divers<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">6.2. Beta diversity<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\"> Beta diversity\ub294 \ub450 \ud658\uacbd \uac04 \ubbf8\uc0dd\ubb3c\uc758 \ucc28\uc774\ub97c \uc758\ubbf8\ud55c\ub2e4. \ub450 \ud658\uacbd\uc744 \ube44\uad50\ud55c \uacb0\uacfc\uc774\uae30 \ub54c\ubb38\uc5d0 2\ucc28\uc6d0 array \ud639\uc740 table \ud615\ud0dc\ub85c \ub370\uc774\ud130\ub97c \ud45c\ud604\ud560 \uc218 \uc788\ub2e4.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\ub450 \uac1c\uccb4\uc758 \ucc28\uc774\ub97c \uce21\uc815\ud558\ub294 \ubc29\ubc95\ub3c4 \ub2e4\uc591\ud560 \uc218 \uc788\ub2e4. \uc774 \ub54c \uc11c\uc5f4\uc758 \uc720\uc0ac\uc131\uae4c\uc9c0 \uace0\ub824\ud574\uc11c \ucc28\uc774\uc810\uc744 \uacc4\uc0b0\ud560 \uc218\ub3c4 \uc788\uc73c\uba70, \uc774 \uacbd\uc6b0 phylogenetic tree\ub97c \uc774\uc6a9\ud560 \uc218\ub3c4 \uc788\ub2e4. \uc5ec\uae30\uc11c\ub294 Bray-Curtis, UniFrac \uac12\uc744 \uacc4\uc0b0\ud55c\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">\n# beta diversity\nqiime diversity beta --i-table intermediate\/feature-table_rarefied.qza --p-metric braycurtis --o-distance-matrix diversity\/braycurtis_dmat.qza\nqiime diversity beta-phylogenetic --i-table intermediate\/feature-table_rarefied.qza --i-phylogeny intermediate\/rooted-tree.qza --p-metric weighted_unifrac --o-distance-matrix diversity\/weighted_unifrac_dmat.qza\n<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">6.3. Diversity\uc640 \uc5f0\uad00\uc131 \ubd84\uc11d<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Diversity\uc640 \uc778\uccb4\uc758 \uc0c1\ud0dc \uac04\uc758 \uad00\ub828\uc131\uc744 \ubd84\uc11d\ud558\uae30 \uc704\ud574\uc11c\ub294 diversity\uc640 \uc5ec\ub7ec \uc9c0\ud45c\uc0ac\uc774\uc758 \uad00\ub828\uc131\uc744 \ubd84\uc11d\ud560 \uc218 \uc788\ub2e4. \uc774\ub294 <code>diversity alpha-group-significance<\/code> \ubc29\ubc95\uc774\ub098, <code>beta-group-significance<\/code>\ubc29\ubc95\uc744 \uc774\uc6a9\ud574 \ubd84\uc11d \ud560 \uc218 \uc788\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\"># Significance group and Visualization \nqiime diversity alpha-group-significance \\\n  --i-alpha-diversity diversity\/shannon_vector.qza \\\n  --m-metadata-file sample-metadata.tsv \\\n  --o-visualization results\/shannon-group-significance.qzv\n\n# Significance group and Visualization \nqiime diversity beta-group-significance \\\n  --i-distance-matrix diversity\/weighted_unifrac_dmat.qza \\\n  --m-metadata-file sample-metadata.tsv \\\n  --m-metadata-column test-grp \\\n  --o-visualization results\/weighted-unifrac-body-site-significance.qzv \\\n  --p-pairwise<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">6.4. Principle Coordinate Analysis<\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">Beta diversity \ub294 \uac1c\uc778 \uac04 \ubbf8\uc0dd\ubb3c \uc720\uc0ac\uc131\/\ucc28\uc774\uc131\uc744 \ub098\ud0c0\ub0b4\ub294 \uc9c0\ud45c\uc774\ub2e4. \ub2e4\ub9cc, \uc5ec\ub7ec \uc0d8\ud50c\uac04\uc758 \ucc28\uc774\ub97c table\ub85c\ub9cc \ud45c\ud604\ud558\uba74 \uad6c\ubd84\uc774 \uc5b4\ub835\uae30 \ub54c\ubb38\uc5d0 2\ucc28\uc6d0\uc73c\ub85c \uc2dc\uac01\ud654\ud574\uc11c \ud55c \ub208\uc5d0 \uc54c\uc544\ubcf4\uae30 \uc27d\uac8c \ud45c\ud604\ud558\ub294 \uac83\uc774 \ubc14\ub78c\uc9c1\ud560 \uac83\uc774\ub2e4. \uc774\ub97c \uc704\ud574 Principle Coordinate Analysis (PCoA) \ubc29\ubc95\uc744 \uc774\uc6a9\ud560 \uc218 \uc788\ub2e4. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">qiime diversity pcoa --i-distance-matrix diversity\/weighted_unifrac_dmat.qza --o-pcoa diversity\/weighted_unifrac_pcoa_result.qza\n\nqiime emperor plot \\\n  --i-pcoa diversity\/weighted_unifrac_pcoa_result.qza \\\n  --m-metadata-file sample-metadata.tsv \\\n  --o-visualization results\/weighted-unifrac-pcoa.qzv<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">(*) <code>emperor plot<\/code>\uc740 PCoA \uacb0\uacfc\ub97c QIIME2 VIEW\ub97c \ud1b5\ud574 \uc2dc\uac01\ud654 \ud560 \uc218 \uc788\ub3c4\ub85d \ub9cc\ub4e4\uc5b4 \uc900\ub2e4. <code>weighted-unifrac-pcoa.qzv<\/code> \ud30c\uc77c\uc744 QIIME2 VIEW \ud398\uc774\uc9c0\uc5d0 \uc5c5\ub85c\ub4dc \ud558\uc5ec PCoA \uacb0\uacfc\ub97c \uc2dc\uac01\ud654 \ud560 \uc218 \uc788\ub2e4. QIIME2 VIEW \ud398\uc774\uc9c0\uc758 \uc8fc\uc18c\ub294 <a href=\"https:\/\/view.qiime2.org\/\">https:\/\/view.qiime2.org\/<\/a>\uc774\ub2e4. <\/p>\n\n\n\n<h3 class=\"wp-block-heading\">7. Taxonomy annotation<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Amplicon sequencing\uc5d0\uc11c \ubbf8\uc0dd\ubb3c\uc740 16S rRNA\uc758 \ubd80\ubd84 \uc11c\uc5f4\ub85c \ud45c\ud604\ub41c\ub2e4. \uadf8\ub9ac\uace0 \uc774 \uc11c\uc5f4\ub85c \ubd80\ud130 \ubbf8\uc0dd\ubb3c\uc758 \uc885\ub958\ub3c4 \uc720\ucd94\ud560 \uc218 \uc788\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\ub2e4\ub9cc, \uc11c\uc5f4\ub85c \ubd80\ud130 \uc720\ucd94\ud560 \uc218 \uc788\ub294 \ubbf8\uc0dd\ubb3c\uc758 \uc218\uc900\uc740 \ucc28\uc774\uac00 \uc788\ub2e4. \ud2b9\uc815 \uc11c\uc5f4\uc774 \ud55c \uc885\uc758 \ubbf8\uc0dd\ubb3c\uc5d0\uc11c\ub9cc \uad00\ucc30\ub41c\ub2e4\uba74, \uc0d8\ud50c\uc5d0\uc11c \ud574\ub2f9 \uc11c\uc5f4\uc774 \uad00\ucc30\ub418\ub294 \uacbd\uc6b0 \uc0d8\ud50c\uc5d0 \ud574\ub2f9 \ubbf8\uc0dd\ubb3c\uc774 \uc874\uc7ac\ud55c\ub2e4\uace0 \uc0dd\uac01\ud560 \uc218 \uc788\ub2e4. \ub2e4\ub9cc, Illumina sequencing \ubc29\ubc95\uc758 \ud55c\uacc4\ub85c \uc778\ud574 \uc6b0\ub9ac\ub294 16S rRNA\uc758 \ubd80\ubd84 \uc11c\uc5f4 \uc815\ubcf4\ub9cc \uac00\uc9c0\uace0 \uc788\ub2e4. \uc774 \uacbd\uc6b0 \uc5ec\ub7ec \uc885\uc758 \ubbf8\uc0dd\ubb3c\uc758 \ub3d9\uc77c\ud55c \uc11c\uc5f4\uc744 \uc9c0\ub2c8\ub294 \uac83\ub3c4 \uac00\ub2a5\ud558\ub2e4. \ub2e4\ub9cc, \uc885\ubcf4\ub2e4 \ud070 \uc218\uc900\uc778 \uc18d(genus)\uc5d0\uc11c \ubcf4\uba74 \ud558\ub098\uc758 \uc18d \ub9cc\uc774 \ud574\ub2f9 \uc11c\uc5f4\uc744 \uac00\uc9c0\ub294 \uacbd\uc6b0\ub3c4 \uc788\uc744 \uc218 \uc788\ub2e4. \uc774 \uacbd\uc6b0, DNA \uc11c\uc5f4\uc5d0\uc11c \uc18d \uc218\uc900\uc758 \uc815\ubcf4\ub97c \uc720\ucd94\ud560 \uc218 \uc788\uc744 \uac83\uc774\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">DNA \uc11c\uc5f4\ub85c \ubd80\ud130 \ubbf8\uc0dd\ubb3c\uc758 \uc885\ub958\ub97c \uc608\uce21\ud558\uae30 \uc704\ud574\uc11c\ub294 \ubbf8\uc0dd\ubb3c\uc758 \uacc4\ud1b5\uc218\ub97c \uc608\uce21\ud558\ub294 \ubaa8\ub378\uc774 \ud544\uc694\ud558\ub2e4. \uc5b4\ub5bb\uac8c \uc608\uce21\ud558\ub294 \ubaa8\ub378\uc744 \ub9cc\ub4e4 \uc218 \uc788\uc744\uc9c0 \uc0dd\uac01\ud574 \ubcf4\uc790.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">7.1. taxonmy annotation <\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">\uc11c\uc5f4\ub85c \ubd80\ud130 \ubbf8\uc0dd\ubb3c\uc758 \uacc4\ud1b5\uc218\ub97c \uc608\uce21\ud55c\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">mkdir taxonomy\nqiime feature-classifier classify-sklearn \\\n  --i-classifier silva-138.1-ssu-nr99-v3v4-classifier.qza \\\n  --i-reads intermediate\/representative_sequences.qza \\\n  --o-classification taxonomy\/taxonomy.qza \\\n  --p-n-jobs 20<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">7.2. Taxonomy visualization <\/h4>\n\n\n\n<p class=\"wp-block-paragraph\">QIIME2\ub97c \uc774\uc6a9\ud574 taxonomy \uc870\uc131\uc744 \uc2dc\uac01\ud654 \ud560 \uc218 \uc788\ub2e4.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Further work<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">\uc774 tutorial\uc5d0\uc11c\ub294 amplicon sequencing \ubd84\uc11d \uacfc\uc815\uc5d0\uc11c \uacf5\ud1b5\uc801\uc73c\ub85c \uc9c4\ud589\ud558\ub294 \ub0b4\uc6a9\uc744 \uc124\uba85\ud558\uc600\ub2e4. \uac01 \uacfc\uc815\uc758 \uc758\ubbf8\uc5d0 \ub300\ud574\uc11c \uc774\ud574\ud558\uace0, \uac01 \uacfc\uc815\uc5d0\uc11c \ud544\uc694\ud55c \uc804\uc0b0\uc801 \ubc29\ubc95\uc774 \ubb34\uc5c7\uc778 \uc0dd\uac01\ud574 \ubcf4\uace0 \uacf5\ubd80\ud558\uc5ec \uc804 \uacfc\uc815\uc744 \uc815\ud655\ud788 \uc774\ud574\ud560 \ud544\uc694\uac00 \uc788\ub2e4.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Introduction Microbimoe\uc740 \ud658\uacbd \uc548\uc5d0 \uc874\uc7ac\ud558\ub294 \ubbf8\uc0dd\ubb3c \uc804\uccb4\ub97c \uc758\ubbf8\ud55c\ub2e4. \ubbf8\uc0dd\ubb3c \uac04 \uc0c1\ud638\uc791\uc6a9 \ubc0f \ubbf8\uc0dd\ubb3c\uacfc \ud658\uacbd\uc758 \uc0c1\ud638\uc791\uc6a9 \uc5f0\uad6c\ub97c \ud1b5\ud574, microbiome\uc758 \uae30\ub2a5\uc744 \uc5f0\uad6c\ud560 \uc218 \uc788\ub2e4. \ud2b9\ud788 \uc0ac\ub78c\uc758 \uc7a5 \ud639\uc740 \ud53c\ubd80 \ub4f1\uc5d0 \uc11c\uc2dd\ud558\ub294 \ubbf8\uc0dd\ubb3c\uc774 \uc778\uccb4\uc758 \uac74\uac15\uacfc \uc9c8\ubcd1\uc5d0 \ubbf8\uce58\ub294 \uc601\ud5a5\uc774 \ud65c\ubc1c\ud558\uac8c \uc5f0\uad6c\ub418\uace0 \uc788\ub2e4. \uc774\ub7ec\ud55c \uc5f0\uad6c\ub97c \uc704\ud574\uc11c\ub294 \ubbf8\uc0dd\ubb3c\uc5d0 \ub300\ud55c \ub370\uc774\ud130\ub97c \ud68d\ub4dd\ud574\uc57c \ud558\ub294\ub370, \ub450 \uac00\uc9c0 NGS \uc2e4\ud5d8 \ubc29\ubc95\uc774 \ub110\ub9ac \uc774\uc6a9\ub41c\ub2e4. Amplicon sequencing\uc740 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":"","_members_access_role":[],"_members_access_error":""},"categories":[27],"tags":[],"class_list":["post-1835","post","type-post","status-publish","format-standard","hentry","category-microbiome"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Tutorial - Microbiome Analysis (amplicon sequencing) - Biomedical Data Science Laboratory<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/tutorial-microbiome-analysis-amplicon-sequencing\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tutorial - Microbiome Analysis (amplicon sequencing) - Biomedical Data Science Laboratory\" \/>\n<meta property=\"og:description\" content=\"Introduction Microbimoe\uc740 \ud658\uacbd \uc548\uc5d0 \uc874\uc7ac\ud558\ub294 \ubbf8\uc0dd\ubb3c \uc804\uccb4\ub97c \uc758\ubbf8\ud55c\ub2e4. \ubbf8\uc0dd\ubb3c \uac04 \uc0c1\ud638\uc791\uc6a9 \ubc0f \ubbf8\uc0dd\ubb3c\uacfc \ud658\uacbd\uc758 \uc0c1\ud638\uc791\uc6a9 \uc5f0\uad6c\ub97c \ud1b5\ud574, microbiome\uc758 \uae30\ub2a5\uc744 \uc5f0\uad6c\ud560 \uc218 \uc788\ub2e4. \ud2b9\ud788 \uc0ac\ub78c\uc758 \uc7a5 \ud639\uc740 \ud53c\ubd80 \ub4f1\uc5d0 \uc11c\uc2dd\ud558\ub294 \ubbf8\uc0dd\ubb3c\uc774 \uc778\uccb4\uc758 \uac74\uac15\uacfc \uc9c8\ubcd1\uc5d0 \ubbf8\uce58\ub294 \uc601\ud5a5\uc774 \ud65c\ubc1c\ud558\uac8c \uc5f0\uad6c\ub418\uace0 \uc788\ub2e4. \uc774\ub7ec\ud55c \uc5f0\uad6c\ub97c \uc704\ud574\uc11c\ub294 \ubbf8\uc0dd\ubb3c\uc5d0 \ub300\ud55c \ub370\uc774\ud130\ub97c \ud68d\ub4dd\ud574\uc57c \ud558\ub294\ub370, \ub450 \uac00\uc9c0 NGS \uc2e4\ud5d8 \ubc29\ubc95\uc774 \ub110\ub9ac \uc774\uc6a9\ub41c\ub2e4. Amplicon sequencing\uc740 [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/tutorial-microbiome-analysis-amplicon-sequencing\/\" \/>\n<meta property=\"og:site_name\" content=\"Biomedical Data Science Laboratory\" \/>\n<meta property=\"article:published_time\" content=\"2023-05-04T08:43:21+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-04-15T06:56:52+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/07\/summary.png\" \/>\n\t<meta property=\"og:image:width\" content=\"3649\" \/>\n\t<meta property=\"og:image:height\" content=\"1547\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"sphong\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"sphong\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"6 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/tutorial-microbiome-analysis-amplicon-sequencing\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/tutorial-microbiome-analysis-amplicon-sequencing\\\/\"},\"author\":{\"name\":\"sphong\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/#\\\/schema\\\/person\\\/8d22f775fcc218b1184ec0d890034e9b\"},\"headline\":\"Tutorial &#8211; 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