{"id":1161,"date":"2022-04-04T15:35:19","date_gmt":"2022-04-04T06:35:19","guid":{"rendered":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/?p=1161"},"modified":"2022-04-04T15:36:36","modified_gmt":"2022-04-04T06:36:36","slug":"post-1161","status":"publish","type":"post","link":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/archives\/1161","title":{"rendered":"BUSCO\u3092\u4f7f\u3046"},"content":{"rendered":"

\u30b2\u30ce\u30e0\u306e\u30a2\u30bb\u30f3\u30d6\u30eb\u306b\u5bfe\u3059\u308b\u8a55\u4fa1\u306e\u4e00\u3064\u306b\u3001\u5fc5\u9808\u907a\u4f1d\u5b50\u304c\u3069\u306e\u3050\u3089\u3044\u898b\u3064\u304b\u308b\u304b\u3068\u3044\u3046\u3082\u306e\u304c\u3042\u308a\u307e\u3059\u3002\u907a\u4f1d\u5b50\u304c\u67d3\u8272\u4f53\u306b\u6563\u5728\u3057\u3066\u3044\u308b\u3068\u4eee\u5b9a\u3057\u3066\u3001\u3042\u308b\u306f\u305a\u306e\u907a\u4f1d\u5b50\u304c\u898b\u3064\u304b\u308b\u5272\u5408\u304c\u30b2\u30ce\u30e0\u5168\u4f53\u306b\u5bfe\u3059\u308b\u30a2\u30bb\u30f3\u30d6\u30eb\u3055\u308c\u305f\u9577\u3055\u306e\u5272\u5408\u3068\u4e00\u81f4\u3059\u308b\u3060\u308d\u3046\u3068\u3044\u3046\u691c\u8a3c\u65b9\u6cd5\u3067\u3059\u3002<\/p>\n

\u3053\u308c\u3092\u5b9f\u73fe\u3059\u308b\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u4e00\u3064\u304cBUSCO (https:\/\/busco.ezlab.org\/)\u3067\u3059\u3002\u305d\u306e\u30d0\u30fc\u30b8\u30e7\u30f35.3.1\u3092docker\u3067\u4f7f\u3063\u3066\u307f\u307e\u3057\u305f\u3002<\/p>\n

docker\u30a4\u30e1\u30fc\u30b8\u306e\u53d6\u5f97<\/h3>\n

\u4ee5\u4e0b\u3082\u305d\u3046\u3067\u3059\u304c\u3001docker\u3092\u4f7f\u3046\u3068\u3053\u308d\u306froot\u3067\u306a\u3044\u3068\u3060\u3081\u3067\u3059\u3002<\/p>\n

# docker search busco  # \u30a4\u30e1\u30fc\u30b8\u3092\u691c\u7d22\nINDEX       NAME                                      DESCRIPTION                                     STARS     OFFICIAL   AUTOMATED\ndocker.io   docker.io\/chrishah\/busco-docker           Docker image containing a full BUSCO install    1                    [OK]\ndocker.io   docker.io\/ezlabgva\/busco                  BUSCO - Benchmarking sets of Universal Sin...   1\ndocker.io   docker.io\/robsyme\/busco                   BUSCO - for  assessing genome assembly and...   1                    [OK]\n(\u4ee5\u4e0b\u7701\u7565)\n# docker pull docker.io\/ezlabgva\/busco:v5.3.1_cv1  # latest\u3067\u306a\u3044\u306e\u3067:tag\u3092\u3064\u3051\u306a\u3044\u3068\u3060\u3081\u3002\u4f7f\u3048\u308b\u30bf\u30b0\u3092\u8abf\u3079\u308b\u65b9\u6cd5\u306f\u306a\u3044\u3068\u601d\u308f\u308c\u308b(\u30a4\u30e1\u30fc\u30b8\u306e\u4f5c\u6210\u8005\u306b\u3042\u305f\u308b\u3057\u304b\u306a\u3044)\u3002\n<\/pre>\n
\u30b3\u30f3\u30c6\u30ca\u306e\u8abf\u67fb<\/h3>\n
\u3068\u308a\u3042\u3048\u305a\u30b3\u30f3\u30c6\u30ca\u5185\u306e\u74b0\u5883\u3092\u8abf\u3079\u308b\u305f\u3081\u306b\u30b7\u30a7\u30eb\u3092\u8d77\u52d5\u3057\u307e\u3059\u3002<\/p>\n
# docker run -it --rm ezlabgva\/busco:v5.3.1_cv1 bash\nbusco_user@3772446d2eee:\/busco_wd$ id\nuid=1000(busco_user) gid=1001(busco_user) groups=1001(busco_user),1000(busco_users)\nbusco_user@3772446d2eee:\/busco_wd$ pwd\n\/busco_wd   # <- \u3053\u308c\u304c\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\nbusco_user@3772446d2eee:\/busco_wd$ busco -h  # \u4f7f\u3044\u65b9\u3092\u8abf\u3079\u308b\nusage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]\n(\u4ee5\u4e0b\u7701\u7565)\nbusco_user@3772446d2eee:\/busco_wd$ busco --list-datasets    # \u4f7f\u7528\u3067\u304d\u308b\u907a\u4f1d\u5b50\u30bb\u30c3\u30c8\n(\u9014\u4e2d\u7701\u7565)\neukaryota_odb10   (\u771f\u6838\u751f\u7269)\n     - viridiplantae_odb10  (\u7dd1\u8272\u690d\u7269\u4e9c\u754c)\n         - embryophyta_odb10    (\u9678\u4e0a\u690d\u7269)\n             - eudicots_odb10    (\u771f\u6b63\u53cc\u5b50\u8449\u985e)\nbusco_user@3772446d2eee:\/busco_wd$ exit   # --rm\u3092\u3064\u3051\u3066\u3044\u308b\u306e\u3067\u81ea\u52d5\u7684\u306b\u30b3\u30f3\u30c6\u30ca\u304c\u524a\u9664\u3055\u308c\u308b\u3002\n<\/pre>\n
BUSCO\u3092\u5b9f\u884c<\/h3>\n
docker\u306e\u8d77\u52d5\u30aa\u30d7\u30b7\u30e7\u30f3<\/h4>\n
BUSCO\u306e\u51fa\u529b\u3092\u30ed\u30fc\u30ab\u30eb\u306e\u30d5\u30a1\u30a4\u30eb\u30b7\u30b9\u30c6\u30e0\u306b\u66f8\u304d\u51fa\u3059\u305f\u3081\u306b\u3001\u30db\u30b9\u30c8\u5074\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3092\u30b3\u30f3\u30c6\u30ca\u5185\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u30de\u30a6\u30f3\u30c8\u3057\u307e\u3059(-v \/home\/takamasa\/busco:\/busco_wd)\u3002
\n\u30b3\u30f3\u30c6\u30ca\u5185\u304b\u3089\u89e3\u6790\u5bfe\u8c61\u306e\u30b2\u30ce\u30e0\u914d\u5217(\/genome_dir\/genome.fa)\u3092\u898b\u3048\u308b\u3088\u3046\u306b\u3059\u308b(-v \/genome_dir:\/busco_wd\/genome_dir)\u3002
\n\u7d50\u679c\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u4e00\u822c\u30e6\u30fc\u30b6\u30fc\u304c\u81ea\u7531\u306b\u3067\u304d\u308b\u3088\u3046\u306b\u3059\u308b(-u takamasa:takamasa)
\n\u6642\u9593\u304c\u304b\u304b\u308b\u306e\u3067\u30d0\u30c3\u30af\u30b0\u30e9\u30a6\u30f3\u30c9\u3067\u5b9f\u884c\u3059\u308b(-d)\u3002\u30d1\u30e9\u30e1\u30fc\u30bf\u30fc\u306e\u8a2d\u5b9a\u304c\u3061\u3083\u3093\u3068\u3067\u304d\u308b\u307e\u3067\u306f-d\u306e\u4ee3\u308f\u308a\u306b-it\u3068\u3064\u3051\u3066\u304a\u304f\u3068\u3044\u3044\u3067\u3057\u3087\u3046\u3002<\/p>\n
busco\u306e\u8d77\u52d5\u30aa\u30d7\u30b7\u30e7\u30f3<\/h4>\n
-f: \u7d50\u679c\u3092\u4e0a\u66f8\u304d\u3059\u308b\u3002\u30a8\u30e9\u30fc\u7d42\u4e86\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3092\u3044\u3061\u3044\u3061\u524a\u9664\u3057\u3066\u304b\u3089\u5b9f\u884c\u3059\u308b\u306e\u304c\u9762\u5012\u306a\u306e\u3067\u3002
\n-i: \u5165\u529b\u30d5\u30a1\u30a4\u30eb\u3002\u30b3\u30f3\u30c6\u30ca\u5185\u3067\u306e\u30d1\u30b9\u3067\u3042\u308b\u3053\u3068\u306b\u6ce8\u610f\u3002
\n-o: \u51fa\u529b\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3002-h\u3067\u306f”Output folders and files will be labelled with this name.”\u3068\u306a\u3063\u3066\u3044\u308b\u304c\u3001\u5b9f\u969b\u306b\u306f\u3053\u306e\u540d\u524d\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u304c\u4f5c\u6210\u3055\u308c\u3066\u3001\u305d\u306e\u4e2d\u306b\u30d5\u30a1\u30a4\u30eb\u304c\u3064\u304f\u3089\u308c\u308b\u3002
\n-m: \u89e3\u6790\u5bfe\u8c61\u306e\u914d\u5217\u306e\u7a2e\u985e\u3002RNA-Seq\u306e\u30a2\u30bb\u30f3\u30d6\u30eb\u3067\u3042\u308c\u3070transcriptome\u3092\u3001\u30a2\u30df\u30ce\u9178\u914d\u5217\u3067\u3042\u308c\u3070proteins\u3092\u6307\u5b9a\u3059\u308b\u3002
\n-l: \u89e3\u6790\u5bfe\u8c61\u306e\u751f\u7269\u306e\u7cfb\u7d71\u3002\u4eca\u56de\u306f\u53cc\u5b50\u8449\u690d\u7269\u3092\u6307\u5b9a\u3057\u305f\u3002–list-databases\u3067\u3067\u3066\u304f\u308b\u540d\u524d\u304b\u3089\u9069\u5f53\u306a\u3082\u306e\u3092\u9078\u3076<\/p>\n
docker run --rm -d -u takamasa:takamasa \\\n    -v \/home\/takamasa\/busco:\/busco_wd \\\n    -v \/genome_dir:\/busco_wd\/genome_dir \\\n    ezlabgva\/busco:v5.3.1_cv1 \\\n    busco -f -i genome_dir\/genome.fa -o out -m genome -l eudicots_odb10\n<\/pre>\n
380Mbp\u306e\u30b2\u30ce\u30e0\u30674.5\u6642\u9593\u304b\u304b\u308a\u307e\u3057\u305f\u3002-c\u30aa\u30d7\u30b7\u30e7\u30f3\u3067\u4f7f\u7528CPU\u6570\u3092\u6307\u5b9a\u3067\u304d\u308b\u3088\u3046\u306a\u306e\u3067\u3001\u3053\u308c\u3092\u5897\u3084\u3059\u3068\u3082\u3046\u5c11\u3057\u901f\u304f\u306a\u308b\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u3002<\/p>\n
\u7d50\u679c\u306e\u89e3\u91c8<\/h3>\n
\/home\/takamasa\/busco\/out \u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306b\u3042\u308bshort_summary.specific.eudicots_odb10.out.txt\u3092\u898b\u308b\u3002<\/p>\n
        ***** Results: *****\n\n        C:56.2%[S:54.6%,D:1.6%],F:5.4%,M:38.4%,n:425\n        239     Complete BUSCOs (C)\n        232     Complete and single-copy BUSCOs (S)\n        7       Complete and duplicated BUSCOs (D)\n        23      Fragmented BUSCOs (F)\n        163     Missing BUSCOs (M)\n        425     Total BUSCO groups searched\n<\/pre>\n
\u8abf\u3079\u305f425\u500b\u306e\u907a\u4f1d\u5b50\u306e\u3046\u3061\u3001239\u500b(232 + 7)\u304c\u30b2\u30ce\u30e0\u306b\u898b\u3064\u304b\u3063\u305f\u3002\u5358\u7d14\u306b\u8a00\u3048\u3070\u3001\u30a2\u30bb\u30f3\u30d6\u30eb\u3055\u308c\u305f\u914d\u5217\u306f\u5168\u4f53\u306e56%\u3060\u3088\u3001\u3068\u3044\u3046\u3053\u3068\u3002<\/p>\n
run_eudicots_odb10<\/h4>\n
\u3053\u3053\u306b\u8a73\u7d30\u306a\u7d50\u679c\u304c\u3042\u308b\u3002full_table.tsv \u3068 missing_busco_list.tsv \u306f\u4f7f\u7528\u3057\u305f\u907a\u4f1d\u5b50\u30bb\u30c3\u30c8\u306e\u3046\u3061\u89e3\u6790\u5bfe\u8c61\u306b\u898b\u3064\u304b\u3063\u305f\u3082\u306e\u3068\u898b\u3064\u304b\u3089\u306a\u304b\u3063\u305f\u3082\u306e\u304c\u66f8\u304b\u308c\u3066\u3044\u308b\u3002
\n\u30b5\u30d6\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306ebusco_sequences\u306b\u306f\u898b\u3064\u304b\u3063\u305f\u30a2\u30df\u30ce\u9178\u914d\u5217\u304c\u3042\u308b\u3002<\/p>\n
\u30d9\u30f3\u30c1\u30de\u30fc\u30af<\/h3>\n
\u3061\u306a\u307f\u306b\u3001\u30b7\u30ed\u30a4\u30cc\u30ca\u30ba\u30ca\u306e\u30b2\u30ce\u30e0\u3092\u8abf\u3079\u3066\u307f\u308b\u3068\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u306a\u308a\u307e\u3057\u305f\u3002<\/p>\n
        ***** Results: *****\n\n        C:99.3%[S:98.6%,D:0.7%],F:0.0%,M:0.7%,n:425\n        422     Complete BUSCOs (C)\n        419     Complete and single-copy BUSCOs (S)\n        3       Complete and duplicated BUSCOs (D)\n        0       Fragmented BUSCOs (F)\n        3       Missing BUSCOs (M)\n        425     Total BUSCO groups searched\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
\u30b2\u30ce\u30e0\u306e\u30a2\u30bb\u30f3\u30d6\u30eb\u306b\u5bfe\u3059\u308b\u8a55\u4fa1\u306e\u4e00\u3064\u306b\u3001\u5fc5\u9808\u907a\u4f1d\u5b50\u304c\u3069\u306e\u3050\u3089\u3044\u898b\u3064\u304b\u308b\u304b\u3068\u3044\u3046\u3082\u306e\u304c\u3042\u308a\u307e\u3059\u3002\u907a\u4f1d\u5b50\u304c\u67d3\u8272\u4f53\u306b\u6563\u5728\u3057\u3066\u3044\u308b\u3068\u4eee\u5b9a\u3057\u3066\u3001\u3042\u308b\u306f\u305a\u306e\u907a\u4f1d\u5b50\u304c\u898b\u3064\u304b\u308b\u5272\u5408\u304c\u30b2\u30ce\u30e0\u5168\u4f53\u306b\u5bfe\u3059\u308b\u30a2\u30bb\u30f3\u30d6\u30eb\u3055\u308c\u305f\u9577\u3055\u306e\u5272\u5408\u3068\u4e00\u81f4\u3059\u308b […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[13,17],"tags":[],"_links":{"self":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts\/1161"}],"collection":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/comments?post=1161"}],"version-history":[{"count":15,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts\/1161\/revisions"}],"predecessor-version":[{"id":1177,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/posts\/1161\/revisions\/1177"}],"wp:attachment":[{"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/media?parent=1161"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/categories?post=1161"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/tags?post=1161"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}