{"id":2332,"date":"2023-07-05T13:20:34","date_gmt":"2023-07-05T04:20:34","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2332"},"modified":"2023-07-05T13:20:38","modified_gmt":"2023-07-05T04:20:38","slug":"bioinfoamplicon_sorter%e3%81%a7nanopore-amplicon-sequence%e3%81%ae%e3%83%87%e3%83%bc%e3%82%bf%e3%82%92de-novo%e3%82%a2%e3%82%bb%e3%83%b3%e3%83%96%e3%83%ab%e3%81%99%e3%82%8b","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2332","title":{"rendered":"[bioinfo]amplicon_sorter\u3067nanopore amplicon sequence\u306e\u30c7\u30fc\u30bf\u3092de novo\u30a2\u30bb\u30f3\u30d6\u30eb\u3059\u308b"},"content":{"rendered":"\n<p>\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u65b9\u6cd5\u306b\u3064\u3044\u3066\u306f\u3001<a rel=\"noreferrer noopener\" href=\"https:\/\/kazumaxneo.hatenablog.com\/entry\/2022\/03\/17\/223852\" target=\"_blank\">\u4e0a\u5742\u3055\u3093\u306e\u60c5\u5831<\/a>\u306b\u5f93\u3063\u305f\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>mamba create -n amplicon_sorter python=3.9 -y\r\nconda activate amplicon_sorter\r\npython3 -m pip install python-Levenshtein\r\npython3 -m pip install edlib\r\npython3 -m pip install biopython\r\npython3 -m pip install matplotlib\r\n\r\n#\u672c\u4f53\r\ngit clone https:\/\/github.com\/avierstr\/amplicon_sorter.git\r\ncdamplicon_sorter\/<\/code><\/pre>\n\n\n\n<p>Nanopore R10.4.1\u306e\u30d5\u30ed\u30fc\u30bb\u30eb\u4e0a\u3067LSK-SQK114\u3067\u4f5c\u3063\u305f\u30e9\u30a4\u30d6\u30e9\u30ea\u3092\u8aad\u3080\u5834\u5408\u3001\u4e0b\u8a18\u306e\u3088\u3046\u306b\u7d50\u69cb\u30af\u30aa\u30ea\u30c6\u30a3\u306f\u9ad8\u3044\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"eager\" decoding=\"async\" width=\"515\" height=\"580\" src=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-125659.jpg\" alt=\"\" class=\"wp-image-2333\" srcset=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-125659.jpg 515w, https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-125659-266x300.jpg 266w\" sizes=\"(max-width: 515px) 100vw, 515px\" \/><\/figure>\n\n\n\n<p>\u304c\u3001qscore > 12\u304c\u63a8\u5968\u3055\u308c\u3066\u3044\u308b\u306e\u3067\u3001NanoFilt\u3067qscore > 12\u3067filtorate\u3059\u308b\u3002pirmer annealing sites\u3092\u78ba\u8a8d\u3057\u305f\u3044\u306e\u3067crop\u306f\u3057\u306a\u3044\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>cat concat.fastq | NanoFilt -q 12 > filtered_concat.fastq<\/code><\/pre>\n\n\n\n<p>amplicon_sorter\u306e\u624b\u9806\u3068\u3057\u3066\u3001\u307e\u305a\u30d2\u30b9\u30c8\u30b0\u30e9\u30e0\u3067\u30ea\u30fc\u30c9\u9577\u306e\u5206\u5e03\u3092\u78ba\u8a8d\u3059\u308b\u3002amplicon\u306e\u5834\u5408\u3001\u76ee\u7684\u7523\u7269\u306e\u30d4\u30fc\u30af\u304c\u5b58\u5728\u3059\u308b\u306f\u305a\u3067\u3042\u308b\u3002\u4eca\u56de\u306eamplicon sequencing\u306e\u5834\u5408\u306f\u3001\u4e8c\u3064\u306e\u7523\u7269\u3092\u6df7\u305c\u3066\u3044\u308b\u306e\u3067\u4e8c\u3064\u306e\u30d4\u30fc\u30af\u304c\u5b58\u5728\u3059\u308b\u3002\u307e\u305a\u77ed\u3044\u65b9\u306f4.8 kb\u304b\u30895.6 kb\u3042\u305f\u308a\u306b\u30d4\u30fc\u30af\u304c\u53ce\u307e\u308b\u3002-min\u3068-max\u3092\u8abf\u6574\u3057\u3066\u3001\u4f55\u5ea6\u304b\u30d2\u30b9\u30c8\u30b0\u30e9\u30e0\u3092\u63cf\u304b\u305b\u3066\u8d64\u70b9\u7dda\u304c\u30d4\u30fc\u30af\u3092\u5305\u542b\u3059\u308b\u3088\u3046\u306b\u3059\u308b\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>python3 amplicon_sorter.py -i filtered_concat.fastq -o amplicon_sorter_out -min 4800 -max 5600 -ho<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"929\" height=\"471\" src=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-130626.jpg\" alt=\"\" class=\"wp-image-2334\" srcset=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-130626.jpg 929w, https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-130626-300x152.jpg 300w, https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-130626-768x389.jpg 768w\" sizes=\"auto, (max-width: 929px) 100vw, 929px\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"713\" height=\"74\" src=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-130953.jpg\" alt=\"\" class=\"wp-image-2335\" srcset=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-130953.jpg 713w, https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-130953-300x31.jpg 300w\" sizes=\"auto, (max-width: 713px) 100vw, 713px\" \/><\/figure>\n\n\n\n<p>\u3053\u308c\u304c\u78ba\u8a8d\u51fa\u6765\u305f\u3089\u3001\u5b9f\u969b\u306b\u30e9\u30f3\u3092\u884c\u3046\u3002\u30c7\u30d5\u30a9\u30eb\u30c8\u3067\u306f\u62bd\u51fa\u3059\u308b\u30ea\u30fc\u30c9\u6570\u304c10000\u3068\u306a\u3063\u3066\u3044\u308b\u3002total evidence\u4fe1\u5949\u8005\u306f\u3053\u306e\u7bc4\u56f2\u306e\u3059\u3079\u3066\u306e\u30c7\u30fc\u30bf\u3092\u4f7f\u3044\u305f\u3044\u306e\u3067&#8221;-maxr 20000&#8243;\u3068\u3057\u3066\u3001\u3059\u3079\u3066\u306e\u30ea\u30fc\u30c9\u3092\u4f7f\u3063\u3066\u30e9\u30f3\u3092\u884c\u3046\u3002&#8221;-np 20&#8243;\u3068\u3057\u3066\u3001core i7 12700KF\u3092\u30d5\u30eb\u306b\u56de\u3057\u306610\u5206\u7a0b\u5ea6\u304b\u304b\u308b\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>python3 amplicon_sorter.py -i filtered_concat.fastq -o amplicon_sorter_out -min 4800 -max 5600 -np 20 -maxr 20000<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"995\" height=\"707\" src=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-131356.jpg\" alt=\"\" class=\"wp-image-2336\" srcset=\"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-131356.jpg 995w, https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-131356-300x213.jpg 300w, https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/wp-content\/uploads\/2023\/07\/\u30b9\u30af\u30ea\u30fc\u30f3\u30b7\u30e7\u30c3\u30c8-2023-07-05-131356-768x546.jpg 768w\" sizes=\"auto, (max-width: 995px) 100vw, 995px\" \/><\/figure>\n\n\n\n<p>\u30ea\u30fc\u30c9\u304c\u3044\u304f\u3064\u304b\u306e\u30b0\u30eb\u30fc\u30d7\u306b\u5206\u3051\u3089\u308c\u3001\u76ee\u7684\u306eamplicon\u306f\u30010.group\u306b\u632f\u308a\u5206\u3051\u3089\u308c\u30668302\u3092\u4f7f\u3063\u3066consensus\u914d\u5217\u304c\u51fa\u529b\u3055\u308c\u308b\u3002\u304a\u305d\u3089\u304f\u6b63\u78ba\u6027\u306b\u95a2\u3057\u3066\u306f\u5341\u5206\u3059\u304e\u308b\u3050\u3089\u3044\u5341\u5206\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u65b9\u6cd5\u306b\u3064\u3044\u3066\u306f\u3001\u4e0a\u5742\u3055\u3093\u306e\u60c5<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"colormag_page_container_layout":"default_layout","colormag_page_sidebar_layout":"default_layout","_locale":"ja","_original_post":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=2332","footnotes":""},"categories":[7],"tags":[],"class_list":["post-2332","post","type-post","status-publish","format-standard","hentry","category-protocol","ja"],"_links":{"self":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/2332","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2332"}],"version-history":[{"count":1,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/2332\/revisions"}],"predecessor-version":[{"id":2337,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/2332\/revisions\/2337"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2332"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2332"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2332"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}