{"id":1775,"date":"2022-03-20T17:10:52","date_gmt":"2022-03-20T08:10:52","guid":{"rendered":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1775"},"modified":"2023-03-30T01:02:32","modified_gmt":"2023-03-29T16:02:32","slug":"bioinfokraken2%e3%82%92%e4%bd%bf%e3%81%a3%e3%81%a6%e3%82%b3%e3%83%b3%e3%82%bf%e3%83%9f%e3%83%aa%e3%83%bc%e3%83%89%e3%82%92%e6%8e%92%e9%99%a4%e3%81%99%e3%82%8b","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1775","title":{"rendered":"[bioinfo]kraken2\u3092\u4f7f\u3063\u3066\u30b3\u30f3\u30bf\u30df\u30ea\u30fc\u30c9\u3092\u6392\u9664\u3059\u308b"},"content":{"rendered":"\n

\u8d85\u4e26\u5217\u30b7\u30fc\u30af\u30a8\u30f3\u30b5\u30fc\u306e\u30c7\u30fc\u30bf\u306b\u304a\u3044\u3066\u30b3\u30f3\u30bf\u30df\u306b\u7531\u6765\u3059\u308b\u30ea\u30fc\u30c9\u306f\u89e3\u6790\u3092\u3059\u308b\u969b\u306b\u69d8\u3005\u306a\u554f\u984c\u3092\u5f15\u304d\u8d77\u3053\u3059\u3002de novo\u30a2\u30bb\u30f3\u30d6\u30eb\u3092\u3059\u308b\u969b\u306b\u3082\u6570\u30d1\u30fc\u30bb\u30f3\u30c8\u306f\u76ee\u7684\u4ee5\u5916\u306e\u30ea\u30fc\u30c9\u304c\u542b\u307e\u308c\u308b\u305f\u3081\u3001\u3053\u308c\u3092\u53d6\u308a\u9664\u304f\u3053\u3068\u3092\u8a66\u307f\u305f\u3002<\/p>\n\n\n\n

kraken2\u3068kraken-tools\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3002kraken2\u306fjellyfish\u3082\u5fc5\u8981\u3068\u3059\u308b\u304c\u3053\u308c\u306f\u5225\u306bpath\u304c\u901a\u3063\u305f\u5834\u6240\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u6e08\u307f\u3068\u3059\u308b\uff08\u4eca\u56de\u306fconda\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\uff09\u3002<\/p>\n\n\n\n

git clone https:\/\/github.com\/DerrickWood\/kraken2\ncd kraken2\n.\/install_kraken2\ncd ..\/\ngit clone https:\/\/github.com\/jenniferlu717\/KrakenTools\ncd KrakenTools\nchmod +x *.py\n <\/pre>\n\n\n\n
kraken2-build\u3067kraken2\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3092\u69cb\u7bc9\u3059\u308b\u3002kraken2\u306b\u306f\u30ab\u30b9\u30bf\u30e0\u3067\u81ea\u5206\u3067\u6c7a\u3081\u305f\u30c7\u30fc\u30bf\u3084ncbi\u306b\u767b\u9332\u3055\u308c\u3066\u3044\u308b\u30c7\u30fc\u30bf\u306a\u3069\u3092\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u306b\u767b\u9332\u3067\u304d\u308b\u304c\u3001\u4eca\u56de\u306f\u30d2\u30c8\u30b2\u30ce\u30e0\u3068\u5fae\u751f\u7269\u30b2\u30ce\u30e0\u306e\u30b3\u30f3\u30bf\u30df\u3092\u691c\u51fa\u3057\u305f\u304b\u3063\u305f\u306e\u3067\u3001standard\u3092\u4f7f\u3063\u305f\u3002\u30c7\u30fc\u30bf\u91cf\u304c\u304b\u306a\u308a\u5927\u304d\u3044\u306e\u3067\u3053\u308c\u3060\u3051\u3067\u3082\u534a\u65e5\u304b\u304b\u308b\u3002<\/p>\n\n\n\n
kraken2-build --standard -db krakendb --threads 8<\/pre>\n\n\n\n
\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u304c\u3067\u304d\u305f\u3089kraken2\u3092\u5b9f\u884c\u3059\u308b\u3002<\/p>\n\n\n\n
kraken2 --threads 12 --quick --db krakendb --paired read_1.fq read_2.fq --report kraken2_output_report > kraken2_out <\/pre>\n\n\n\n
kraken-tools\u306eextract_kraken_reads.py\u3067\u5143\u306e\u30c7\u30fc\u30bf\u304b\u3089\u30b3\u30f3\u30bf\u30df\u3092\u53d6\u308a\u9664\u3044\u305f\u3082\u306e\u3092\u62bd\u51fa\u3059\u308b\u3002\u4eca\u56de\u306fhuman\u3067\u3082\u3001\u7d30\u83cc\u3001\u30a6\u30a3\u30eb\u30b9\u3067\u3082\u306a\u3044\u30ea\u30fc\u30c9\u3092\u53d6\u308a\u9664\u304d\u305f\u304b\u3063\u305f\u306e\u3067\u3001classified\u3055\u308c\u3066\u3044\u306a\u3044\u3001unknown\u306e\u30ea\u30fc\u30c9\u3092\u62bd\u51fa\u3057\u305f\u3002–max\u3092\u6307\u5b9a\u3057\u306a\u3044\u3068100 M\u30ea\u30fc\u30c9\u4ee5\u4e0a\u306f\u30aa\u30df\u30c3\u30c8\u3055\u308c\u3066\u3057\u307e\u3046\u3088\u3046\u3060\u3002<\/p>\n\n\n\n
extract_kraken_reads.py -k kraken_out -s1 read_1.fq -s2 read_2.fq -o read_krakened_1.fq -o2 read_krakened_2.fq -t 0 --fastq-output --max 300000000<\/pre>\n\n\n\n
\n\n\n\n
2023\/03\/30\u3000\u8ffd\u8a18<\/p>\n\n\n\n
nanopore\u3092\u4f7f\u3063\u305f16S\u30b7\u30fc\u30b1\u30f3\u30b9\u306e\u305f\u3081\u306bsilva\u306e16S\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3092\u69cb\u7bc9\u3057\u305f\u3002<\/p>\n\n\n\n
kraken2-vuild -db silva_16s --type silva<\/pre>\n\n\n\n
\u3057\u304b\u3057\u306a\u304c\u3089\u3001standard\u3067\u306eclassification\u306e\u65b9\u304c\u6210\u7e3e\u304c\u826f\u304b\u3063\u305f\uff08\u4f8b\u3048\u3070\u3001\u3042\u308b\u30b5\u30f3\u30d7\u30eb\u306fstandard\u306780% classified\u306b\u5bfe\u3057\u3066\u300116S_silva\u306f24%\u7a0b\u5ea6\u3067\u3042\u3063\u305f\uff09\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
\u8d85\u4e26\u5217\u30b7\u30fc\u30af\u30a8\u30f3\u30b5\u30fc\u306e\u30c7\u30fc\u30bf\u306b\u304a\u3044\u3066\u30b3\u30f3<\/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=1775","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1775","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\/1775","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=1775"}],"version-history":[{"count":3,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1775\/revisions"}],"predecessor-version":[{"id":2214,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1775\/revisions\/2214"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1775"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1775"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1775"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}