{"id":1219,"date":"2020-03-28T18:41:51","date_gmt":"2020-03-28T09:41:51","guid":{"rendered":"http:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1219"},"modified":"2020-03-30T20:55:10","modified_gmt":"2020-03-30T11:55:10","slug":"bioinfoflappie-flip-flop-basecaller-for-oxford-nanopore-reads-%e3%82%92ubuntu-18-04%e4%b8%8a%e3%81%ab%e3%82%a4%e3%83%b3%e3%82%b9%e3%83%88%e3%83%bc%e3%83%ab%e3%81%99%e3%82%8b","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1219","title":{"rendered":"[bioinfo]Flappie (Flip-flop basecaller for Oxford Nanopore reads) \u3092Ubuntu 18.04\u4e0a\u306b\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b"},"content":{"rendered":"\n<p>Nanopore \u30b7\u30fc\u30af\u30a8\u30f3\u30b5\u30fc\u304b\u3089\u306eraw\u30c7\u30fc\u30bf (fast5)\u306ebasecaller\u306e\u3046\u3061\u3001\u6700\u3082\u7cbe\u5ea6\u304c\u9ad8\u3044\u3068\u3055\u308c\u3066\u3044\u308bFlappie\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u3002<\/p>\n<p>\u307e\u305a\u3001<a href=\"https:\/\/git-lfs.github.com\/\">git lfs (An open source Git extension for versioning large files)<\/a>\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u304a\u304f\u3002<\/p>\n<pre class=\"\">git lfs install<code><br \/><\/code><\/pre>\n<p>\u305d\u306e\u4ed6\u306b\u3001<\/p>\n<ul>\n<li><a href=\"https:\/\/cmake.org\/\" rel=\"nofollow\">Cmake<\/a> for building<\/li>\n<li><a href=\"http:\/\/cunit.sourceforge.net\/\" rel=\"nofollow\">CUnit<\/a> library for unit testing<\/li>\n<li><a href=\"https:\/\/www.hdfgroup.org\/\" rel=\"nofollow\">HDF5<\/a> library<\/li>\n<li><a href=\"https:\/\/www.openblas.net\/\" rel=\"nofollow\">OpenBLAS<\/a> library for linear algebr<\/li>\n<\/ul>\n<p>\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3002<\/p>\n<pre class=\"\">sudo apt install libcunit1 libhdf5 libopenblas-base libunit1-dev libhdf5-dev libopenblas-dev<\/pre>\n<p>Ubuntu 18.04\u306e\u5834\u5408\u3001HDF5\u306e\u30b7\u30f3\u30dc\u30ea\u30c3\u30af\u30ea\u30f3\u30af\u306e\u540d\u524d\u304c\u7570\u306a\u308a\u3001\u5834\u6240\u304c\u308f\u304b\u3089\u306a\u3044\u3068\u3044\u3046\u30a8\u30e9\u30fc\u304c\u51fa\u308b\u306e\u3067\u3001CMakelist.txt\u4e2d\u306b\u3001<\/p>\n<pre class=\"\">set (HDF5 hdf5_serial) <\/pre>\n<p>\u3092\u633f\u5165\u3059\u308b\u306e\u3068\u3001#Find right hdf5 file\u306e\u9805\u76ee\u3092\u4ee5\u4e0b\u306e\u5185\u5bb9\u306b\u5909\u66f4\u3059\u308b\u3002<\/p>\n<pre class=\"\"># Find right hdf5 file<br \/>include (CheckIncludeFile)<br \/>check_include_file (\"\/usr\/include\/hdf5\/serial\/hdf5.h\" HDF5_STANDARD)<br \/>if (HDF5_STANDARD)<br \/>set (HDF5 \"hdf5\")<br \/>else (HDF5_STANDARD)<br \/>check_include_file (\"hdf5\/serial\/hdf5.h\" HDF5_SERIAL)<br \/>if (HDF5_SERIAL)<br \/>set (HDF5 \"hdf5_serial\")<br \/>include_directories (\"\/usr\/include\/hdf5\/serial\")<br \/>endif (HDF5_SERIAL)<br \/>endif (HDF5_STANDARD)<\/pre>\n<p>\u305d\u306e\u4e0a\u3067\u3001<\/p>\n<pre class=\"\">hdf5Root=\/usr\/include\/hdf5\/serial\/ make flappie<\/pre>\n<p>\u3067make\u3002<\/p>\n<p>flappie\u306f\u4ee5\u524d\u306esingle fast5 out put \u306b\u306e\u307f\u5bfe\u5fdc\u3059\u308b\u306e\u3067\u3001ont_fast5_api\u3067multiple fast5\u3092\u5909\u63db\u3059\u308b\u3002<\/p>\n<p>ont_fast5_api\u306fpip\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3002<\/p>\n<pre class=\"\">pip install ont-fast5-api<\/pre>\n<p>\u8907\u6570\u306efast5\u304b\u3089single fast5\u3078\u5909\u63db<\/p>\n<pre class=\"\">multi_to_single_fast5\n    -i, --input_path &lt;(path) folder containing multi_read_fast5 files&gt;\n    -s, --save_path &lt;(path) to folder where single_read fast5 files will be output&gt;\n    [optional] -t, --threads &lt;(int) number of CPU threads to use; default=1&gt;\n    [optional] --recursive &lt;if included, recursively search sub-directories for multi_read files&gt;<\/pre>\n<pre class=\"\">multi_to_single_fast5 -i fast5_pass\/ -s raw\/reads<\/pre>\n<p>\u5b9f\u969b\u306b\u5909\u63db\u3092\u30c8\u30e9\u30a4\u3057\u3066\u307f\u305f\u304c\u9045\u3059\u304e\u3066\u4f7f\u3044\u7269\u306b\u306a\u3089\u306a\u3044&#8230;<\/p>\n","protected":false},"excerpt":{"rendered":"","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":"http:\/\/home.hiroshima-u.ac.jp\/~tigawa\/?p=1219","footnotes":""},"categories":[7],"tags":[],"class_list":["post-1219","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\/1219","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=1219"}],"version-history":[{"count":7,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1219\/revisions"}],"predecessor-version":[{"id":1229,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=\/wp\/v2\/posts\/1219\/revisions\/1229"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1219"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1219"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~tigawa\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1219"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}