{"id":89,"date":"2021-10-19T23:59:02","date_gmt":"2021-10-19T15:59:02","guid":{"rendered":"https:\/\/linguopeng.top\/?p=89"},"modified":"2021-10-19T23:59:45","modified_gmt":"2021-10-19T15:59:45","slug":"kingfisher%e4%b8%80%e4%b8%aa%e9%ab%98%e9%80%9a%e9%87%8f%e6%b5%8b%e5%ba%8f%e6%95%b0%e6%8d%ae%e4%b8%8b%e8%bd%bd%e5%b7%a5%e5%85%b7","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=89","title":{"rendered":"Kingfisher\u4e00\u4e2a\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6570\u636e\u4e0b\u8f7d\u5de5\u5177"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>Kingfisher\u7b80\u4ecb\n    Kingfisher\u662f\u4e00\u4e2a\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6570\u636e\u4e0b\u8f7d\u5de5\u5177\uff0c\u7528\u6237\u63d0\u4f9bRun accessions\u6216\u8005BioProject accessions\uff0c\u5373\u53ef\u5728ENA\u3001SRA\u3001Amazon AWS\u4ee5\u53caGoogle Cloud\u7b49\u6570\u636e\u5e93\u4e2d\u4e0b\u8f7d\u76ee\u6807\u6570\u636e\u3002Kingfisher\u4f1a\u5c1d\u8bd5\u4ece\u4e00\u7cfb\u5217\u7684\u6570\u636e\u6e90\u8fdb\u884c\u6570\u636e\u4e0b\u8f7d\uff0c\u76f4\u5230\u67d0\u4e2a\u6e90\u80fd\u591fwork\u3002\n    \u6b64\u5916\uff0c\u8fd8\u80fd\u6839\u636e\u7528\u6237\u7684\u9700\u6c42\u5c06\u4e0b\u8f7d\u6570\u636e\u76f4\u63a5\u8f93\u51fa\u4e3aSRA\u3001Fastq\u3001Fasta\u6216Gzip\u7b49\u683c\u5f0f\uff0c\u975e\u5e38\u65b9\u4fbf\uff0c\u4e0d\u9700\u8981\u81ea\u5df1\u518d\u5bf9SRA\u6570\u636e\u901a\u8fc7fasterq-dump\u8fdb\u884c\u62c6\u5206\u8f6c\u6362\u3002\nKingfisher\u5b89\u88c5\u4e0e\u4f7f\u7528\n1.\u5b89\u88c5\nconda create -c conda-forge -c bioconda -n kingfisher pigz python extern curl sra-tools pandas requests aria2\nconda activate kingfisher\n#\u4f7f\u7528conda activate\u4e0d\u80fd\u6210\u529f\u6fc0\u6d3b\u73af\u5883\u65f6\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\uff1asource activate kingfisher\npip install bird_tool_utils'>='0.2.17\ngit clone https:\/\/github.com\/wwood\/kingfisher-download\ncd kingfisher-download\/bin\nexport PATH=$PWD:$PATH\nkingfisher -h\n#\u5f39\u51fa\u5e2e\u52a9\u6587\u6863\u5373\u5b89\u88c5\u6210\u529f\n\n2.\u4e0b\u8f7d\u6570\u636e\n\u6ce8\u610f\uff1a\u5982\u679c\u53ea\u60f3\u4e0b\u8f7d\u67d0\u4e2a\u786e\u5b9a\u7684SRA\u6570\u636e\uff0c\u5219\u4f7f\u7528-r\u53c2\u6570\uff0c\u63d0\u4f9bSRR Number\u5373\u53ef\uff0c\u5982 SRR12042866 \uff1b\u82e5\u662f\u60f3\u6279\u91cf\u4e0b\u8f7d\u67d0\u4e2aBioProject\u4e2d\u7684\u6240\u6709\u6570\u636e\uff0c\u5219\u53ef\u4ee5\u4f7f\u7528-p\u53c2\u6570\uff0c\u63d0\u4f9bBioProject Number\uff0c\u5982PRJNA640275\u6216SRP267791\u3002\n\nkingfisher get -r SRP267791 -m ena-ascp ena-ftp prefetch aws-http\n#-r Run number(s) to download\/extract e.g. ERR1739691\n#-p BioProject IDs number(s) to download\/extract from e.g. PRJNA621514 or SRP260223\n\n# -m ena-ascp\u3001ena-ftp\u3001prefetch\u3001aws-http\u3001aws-cp\u3001gcp-cp\n\n# --download-threads \u7ebf\u7a0b\u6570\n\n\u6570\u636e\u4e0b\u8f7d\u6e90\u4ecb\u7ecd\uff08-m\u53c2\u6570\uff09\nena-ascp,\u8c03\u7528Aspera\u4eceENA\u4e2d\u4e0b\u8f7d.fastq.gz\u6570\u636e\nena-ftp\uff0c\u8c03\u7528curl\u4eceENA\u4e2d\u4e0b\u8f7d.fastq.gz\u6570\u636e\nprefetch\uff0c\u8c03\u7528prefetch\u4eceNCBI SRA\u6570\u636e\u5e93\u4e2d\u4e0b\u8f7dSRA\u6570\u636e\uff0c\u7136\u540e\u9ed8\u8ba4\u4f7f\u7528fasterq-dump\u5bf9\u5176\u8fdb\u884c\u62c6\u5206\u8f6c\u6362\naws-http\uff0c\u8c03\u7528aria2c\u4eceAWS Open Data Program\u4e2d\u4e0b\u8f7dSRA\u6570\u636e\uff0c\u7136\u540e\u9ed8\u8ba4\u4f7f\u7528fasterq-dump\u5bf9\u5176\u8fdb\u884c\u62c6\u5206\u8f6c\u6362\n\u4e5f\u5c31\u662f\u8bf4\uff0c\u5982\u679c\u662f\u7528\u7684ENA\u6e90 \u76f4\u63a5\u4e0b\u8f7d\u7684\u5c31\u662ffastq\uff0c\u5982\u679c\u7528\u7684SRA\u6216\u5176\u4ed6\uff0c\u90a3\u5c31\u662f\u4e0b\u8f7dSRA\u6570\u636e  \u7136\u540ekingfisher\u518d\u81ea\u52a8\u8c03\u7528fasterq-dump\u8f6c\u6362\u6210fastq\nSRA\u683c\u5f0f\u8f6c\u6362\u6210fastq\u683c\u5f0f\uff0c\u8c03\u7528fasterq-dump\n\nkingfisher extract --sra SRR1574780.sra -t 20 -f fastq.gz\n#-f,\u6307\u5b9a\u8f6c\u6362\u8f93\u51fa\u7684\u6587\u4ef6\u683c\u5f0f\uff0c\u652f\u6301fastq,fastq.gz,fasta,fasta.gz\n#-t\uff0c\u6307\u5b9a\u7ebf\u7a0b\u6570<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[12],"class_list":["post-89","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-linux"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/89","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=89"}],"version-history":[{"count":2,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/89\/revisions"}],"predecessor-version":[{"id":91,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/89\/revisions\/91"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=89"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=89"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=89"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}