{"id":25822,"date":"2024-01-23T17:28:09","date_gmt":"2024-01-23T09:28:09","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25822"},"modified":"2024-01-23T17:28:11","modified_gmt":"2024-01-23T09:28:11","slug":"metaphlan-4-%e5%ae%8f%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%89%a9%e7%a7%8d%e6%b3%a8%e9%87%8a%e5%b7%a5%e5%85%b7","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25822","title":{"rendered":"MetaPhlAn 4\u2014\u5b8f\u57fa\u56e0\u7ec4\u7269\u79cd\u6ce8\u91ca\u5de5\u5177"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5e26\u6765\u4e00\u6b3e\u975e\u5e38\u65b0\u7684\uff0c\u4f46\u662f\u529f\u80fd\u975e\u5e38\u5f3a\u5927\u7684\u751f\u4fe1\u5206\u6790\u5de5\u5177– MetaPhlAn 4\u3002<\/p>\n

<\/p>\n

MetaPhlAn\u662f\u4e00\u79cd\u8ba1\u7b97\u5de5\u5177\uff0c\u7528\u4e8e\u4ece\u5143\u57fa\u56e0\u7ec4\u9730\u5f39\u67aa\u6d4b\u5e8f\u6570\u636e\uff08\u5373\u975e16S\uff09\u4e5f\u5c31\u662f\u5b8f\u57fa\u56e0\u7ec4\u6570\u636e\u4e2d\u5206\u6790\u7269\u79cd\u7ea7\u5fae\u751f\u7269\u7fa4\u843d\uff08\u7ec6\u83cc\u3001\u53e4\u7ec6\u83cc\u548c\u771f\u6838\u751f\u7269\uff09\u7684\u7ec4\u6210\u3002\u6700\u65b0\u7248\u7684MetaPhlAn 4\u53d1\u8868\u57282023\u5e742\u670823\u65e5\u300aNature Biotechnology\u300b\u671f\u520a\u4e0a\u3002MetaPhlAn 4\u5229\u7528\u5df2\u77e5\u5fae\u751f\u7269\u57fa\u56e0\u7ec4\u548cMAGs\u7684\u7ec4\u5408\u6269\u5c55\u96c6\uff0c\u5b9a\u4e49\u4e86\u7269\u79cd\u6c34\u5e73\u4e0a\u7684\u57fa\u56e0\u7ec4\u7bb1\uff08SGBs\uff09\uff0c\u4ee5\u8fdb\u884c\u66f4\u5168\u9762\u7684\u5b8f\u57fa\u56e0\u7ec4\u5206\u7c7b\u5b66\u5206\u6790\u3002\u4ece101\u4e07\u4e2a\u539f\u6838\u751f\u7269\u53c2\u8003\u57fa\u56e0\u7ec4\u548c\u5b8f\u57fa\u56e0\u7ec4\u7ec4\u88c5\u57fa\u56e0\u7ec4\u7684\u96c6\u5408\u4e2d\uff0c\u5728\u7269\u79cd\u6c34\u5e73\u4e3a26970\u4e2a\u57fa\u56e0\u7ec4\u7bb1\u5b9a\u4e49\u4e86\u7279\u5f02\u6027\u7684\u6807\u8bb0\u57fa\u56e0\uff0c\u5176\u4e2d4992\u4e2a\u5728\u7269\u79cd\u6c34\u5e73\u4e0a\u5c1a\u672a\u5206\u7c7b\u3002MetaPhlAn 4\u5728\u5168\u7403\u4eba\u7c7b\u80a0\u9053\u5fae\u751f\u7269\u4e2d\u589e\u52a0\u4e86\u7ea620%\u7684\u77ed\u5e8f\u5217\u7269\u79cd\u6ce8\u91ca\uff0c\u800c\u5728\u5c1a\u672a\u5145\u5206\u7814\u7a76\u7684\u73af\u5883\uff08\u5982\u53cd\u520d\u52a8\u7269\u7624\u80c3\u5fae\u751f\u7269\u7ec4\u7b49\uff09\u4e2d\u589e\u52a0\u4e8640%\u3002MetaPhlAn 4\u5728\u7efc\u5408\u8bc4\u4f30\u5206\u6790\u65b9\u9762\u6bd4\u73b0\u6709\u53ef\u66ff\u4ee3\u65b9\u6848\u66f4\u51c6\u786e\uff0c\u540c\u65f6\u8fd8\u53ef\u4ee5\u5bf9\u672a\u57f9\u517b\u5206\u79bb\u7684\u751f\u7269\u4f53\u8fdb\u884c\u51c6\u786e\u5b9a\u91cf\u3002\u603b\u800c\u8a00\u4e4b\uff0cMetaPhlAn 4\u662f\u5b8f\u57fa\u56e0\u7ec4\u7269\u79cd\u6ce8\u91ca\u4e2d\u4e00\u4e2a\u65b9\u4fbf\u800c\u4e14\u51c6\u786e\u7684\u6700\u65b0\u5de5\u5177\u3002<\/p>\n

\u63a5\u4e0b\u6765\u5c0f\u679c\u5c31\u4e3a\u5927\u5bb6\u5e26\u6765MetaPhlAn 4\u7684\u5b89\u88c5\u548c\u4f7f\u7528\u6559\u7a0b\uff0c\u4e0b\u9762\u7684\u64cd\u4f5c\u90fd\u8981\u5728\u670d\u52a1\u5668\u4e0a\u8fdb\u884c\uff0c\u5982\u679c\u6ca1\u6709\u670d\u52a1\u5668\uff0c\u90a3\u5c0f\u679c\u4e5f\u6ca1\u6cd5\u5566\u3002<\/p>\n

\u4e00\u3001\u521b\u5efaconda\u73af\u5883<\/h2>\n

conda create –name mpa -c bioconda python=3.7<\/p>\n

\u521b\u5efa\u4e00\u4e2a\u540d\u53ebmpa\u7684\u73af\u5883<\/p>\n

\u4e8c\u3001\u5b89\u88c5metaphlan4<\/h2>\n

source activate mpa<\/p>\n

conda install -c bioconda metaphlan<\/p>\n

\u8fd9\u4e00\u6b65\u53ef\u80fd\u4f1a\u5b89\u88c5\u5f88\u4e45\uff0c\u6709\u65f6\u5019\u53ef\u80fd\u4f1a\u51fa\u73b0\u5b89\u88c5\u4e0d\u4e0a\u7684\u95ee\u9898\uff0c\u8fd9\u65f6\u5019\u6211\u4eec\u53ef\u4ee5\u7528pip\u6765\u5b89\u88c5\u3002<\/p>\n

\u4e09\u3001\u5b89\u88c5\u6570\u636e\u5e93<\/h2>\n

metaphlan –install<\/p>\n

\u8fd9\u662f\u6700\u9ebb\u70e6\u7684\u4e00\u6b65\uff08\u4e00\u822c\u7528\u8fd9\u4e2a\u547d\u4ee4\u90fd\u5b89\u88c5\u4e0d\u4e0a\uff09\uff0c\u4e0b\u8f7d\u901f\u5ea6\u8f83\u6162\u4e14\u603b\u517120\u591aG\uff0c\u5efa\u8bae\u53bb\u5b98\u7f51\u4e0b\u8f7d\uff0c\u4e0b\u8f7d\u6700\u65b0\u7684\u90a3\u4e2a\u6570\u636e\u5e93\u3002<\/p>\n

\u8fd9\u516d\u4e2a\u6587\u4ef6\u5efa\u8bae\u90fd\u4e0b\u8f7d\uff0c\u7f51\u5740\u5206\u522b\u662f\uff1a<\/p>\n

http:\/\/cmprod1.cibio.unitn.it\/biobakery4\/metaphlan_databases\/<\/p>\n

http:\/\/cmprod1.cibio.unitn.it\/biobakery4\/metaphlan_databases\/bowtie2_indexes\/<\/a><\/p>\n

<\/p>\n

<\/p>\n

\u8fd9\u51e0\u4e2a\u6587\u4ef6\u5168\u90e8\u90fd\u8981\u653e\u5728metaphlan_databases\u8fd9\u4e2a\u6587\u4ef6\u5939\u91cc\u9762\uff0c\u8def\u5f84\u4e00\u822c\u662f\u8fd9\u4e2a\uff1a<\/p>\n

path\/to\/anaconda3\/envs\/mpa\/lib\/python3.7\/site-packages\/metaphlan\/metaphlan_databases<\/p>\n

\u6ce8\u610f\u6211\u524d\u9762\u8fd9\u4e2apath\/to\/\u662f\u5927\u5bb6\u653eanaconda3\u7684\u6587\u4ef6\u8def\u5f84\u3002<\/p>\n

\u540e\u9762\u8fd0\u884cmetaphlan4\u8dd1\u4e00\u4e2a\u6570\u636e\u5c31\u4f1a\u81ea\u52a8\u5efa\u5e93\u3002\u5efa\u5e93\u540e\u7684metaphlan_databases\u5c31\u6709\u8fd9\u4e9b\u6587\u4ef6\uff1a<\/p>\n

<\/p>\n

\u6ce8\u610fmpa_latest\u8fd9\u4e2a\u6587\u4ef6\uff0c\u5982\u679c\u60a8\u6ca1\u6709\u7684\u8bdd\uff0c\u53ef\u4ee5\u81ea\u5df1vim\u5199\u4e00\u4e2a\uff0c\u91cc\u9762\u7684\u5185\u5bb9\u4e5f\u5c31\u662f\u4e0b\u8f7d\u7684\u6570\u636e\u5e93\u7684\u540d\u5b57\uff1a<\/p>\n

<\/p>\n

\u56db\u3001\u8fd0\u884c<\/h2>\n

\u53cc\u7aef\u6570\u636e\uff1a<\/p>\n

metaphlan *.fastq1,*.fastq2 –input_type fastq -o *.txt –nproc 10 –stat_q 0.1 –bowtie2out bowtie2out_*.bz2<\/p>\n

\u4e5f\u53ef\u4ee5\u5355\u7aef\uff0c\u5c31\u53ea\u8f93\u5165\u4e00\u4e2afastq\u6570\u636e\uff0c\u6ce8\u610ffastq1\u548cfastq2\u4e4b\u95f4\u6709\u4e2a\u9017\u53f7\u3002<\/p>\n

\u5176\u4e2d\u53c2\u6570\u7684\u542b\u4e49\uff1a<\/p>\n

–input_type\u8f93\u5165\u6570\u636e\u7c7b\u578b<\/p>\n

–stat_q\u8d8a\u4f4e\u5047\u9633\u6027\u7387\u8d8a\u9ad8\uff0c\u9ed8\u8ba4\u662f0.2\uff0c\u4f46\u662f\u53ef\u4ee5\u6309\u7167\u6570\u636e\u5177\u4f53\u60c5\u51b5\u8c03\u6574\uff0c0.1\u5e94\u8be5\u662f\u53ef\u4ee5\u63a5\u53d7\u7684<\/p>\n

–nproc\u7ebf\u7a0b<\/p>\n

\u4e94\u3001\u6570\u636e\u5408\u5e76\u622a\u53d6<\/h2>\n

\u591a\u4e2a\u6570\u636e\u8fd0\u884c\u5b8c\u6210\u540e\uff0c\u9700\u8981\u5bf9\u591a\u4e2a\u7ed3\u679c\u8fdb\u884c\u5408\u5e76\uff08\u4e0d\u540c\u7248\u672c\u7684\u6570\u636e\u4e0d\u80fd\u5408\u5e76\uff09 \uff1a<\/p>\n

merge_metaphlan_tables.py metaphlan_output*.txt > output\/merged_abundance_table.txt<\/p>\n

#\u7b5b\u9009\u51fa\u4e0d\u540c\u6c34\u5e73\u7269\u79cd\u4e30\u5ea6\u8868\u683c<\/p>\n

grep -E ‘(s__)|(clade_name)’ merged_abundance_table.txt |grep -v ‘t__’|sed ‘s\/^.*s__\/\/g’|sed ‘s\/\\ \\ \/\\ \/g’|sed ‘s\/\\ \/\\t\/g’ > merged_abundance_table_species.txt<\/p>\n

grep -E ‘(g__)|(clade_name)’ merged_abundance_table.txt |grep -v ‘s__’|sed ‘s\/^.*g__\/\/g’|sed ‘s\/\\ \\ \/\\ \/g’|sed ‘s\/\\ \/\\t\/g’ > merged_abundance_table_genus.txt<\/p>\n

grep -E ‘(f__)|(clade_name)’ merged_abundance_table.txt |grep -v ‘g__’|sed ‘s\/^.*f__\/\/g’|sed ‘s\/\\ \\ \/\\ \/g’|sed ‘s\/\\ \/\\t\/g’ > merged_abundance_table_family.txt<\/p>\n

grep -E ‘(o__)|(clade_name)’ merged_abundance_table.txt |grep -v ‘f__’|sed ‘s\/^.*o__\/\/g’|sed ‘s\/\\ \\ \/\\ \/g’|sed ‘s\/\\ \/\\t\/g’ > merged_abundance_table_order.txt<\/p>\n

grep -E ‘(c__)|(clade_name)’ merged_abundance_table.txt |grep -v ‘o__’|sed ‘s\/^.*c__\/\/g’|sed ‘s\/\\ \\ \/\\ \/g’|sed ‘s\/\\ \/\\t\/g’ > merged_abundance_table_class.txt<\/p>\n

grep -E ‘(p__)|(clade_name)’ merged_abundance_table.txt |grep -v ‘c__’|sed ‘s\/^.*p__\/\/g’|sed ‘s\/\\ \\ \/\\ \/g’|sed ‘s\/\\ \/\\t\/g’ > merged_abundance_table_phylum.txt<\/p>\n

\u516d\u3001\u811a\u672c<\/h2>\n

\u5927\u5bb6\u53ef\u4ee5\u4e00\u4e2a\u4e00\u4e2a\u6570\u636e\u7684\u8dd1\uff0c\u5f53\u7136\u4e5f\u53ef\u4ee5\u5199\u4e2a\u5faa\u73af\uff0c\u8fd9\u6837\u6548\u7387\u66f4\u9ad8\uff0c\u8fd9\u4e2a\u662f\u5c0f\u679c\u81ea\u5df1\u5199\u7684\u4e00\u4e2a\u6700\u7b80\u5355\u7684shell\u811a\u672c\uff1a<\/p>\n

for i in `ls data\/split`; do<\/p>\n

metaphlan data\/${i}_1.fq.gz,data\/${i}_2.fq.gz –input_type fastq –nproc 30 \u2013output metaphlan\/${i}.txt –bowtie2out metaphlan-1\/${i}.bowtie –stat_q 0.05; done<\/p>\n

###split\u6587\u4ef6\u5939\u91cc\u9762\u662f\u6240\u6709\u6570\u636e\u540d\u79f0\u7684\u6587\u4ef6<\/p>\n

\u8fd0\u884c\u5b8c\u7684\u7ed3\u679c\u5927\u6982\u662f\u8fd9\u6837\uff1a
\n<\/p>\n

\u8fd9\u5c31\u662f\u672c\u6b21\u6559\u7a0b\u7684\u5168\u90e8\u5185\u5bb9\u5566\uff0c\u540e\u7eed\u5c0f\u679c\u4f1a\u4e3a\u5927\u5bb6\u5e26\u6765\u66f4\u591a\u7684\u5b8f\u57fa\u56e0\u7ec4\u548c\u6269\u589e\u5b50\u8f6f\u4ef6\u7684\u4f7f\u7528\u6559\u7a0b\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u4e3a\u5927\u5bb6\u5e26\u6765\u4e00\u6b3e\u975e\u5e38\u65b0\u7684\uff0c\u4f46\u662f\u529f\u80fd\u975e\u5e38\u5f3a\u5927\u7684\u751f\u4fe1\u5206\u6790\u5de5\u5177– MetaPhlAn 4\u3002 Met […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25822"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=25822"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25822\/revisions"}],"predecessor-version":[{"id":25829,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/25822\/revisions\/25829"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25822"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25822"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25822"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}