{"id":2703,"date":"2019-04-07T14:58:02","date_gmt":"2019-04-07T06:58:02","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2703"},"modified":"2019-04-10T00:08:08","modified_gmt":"2019-04-09T16:08:08","slug":"%e4%bd%bf%e7%94%a8diamond%e5%b0%86%e5%85%a8%e5%9f%ba%e5%9b%a0%e7%bb%84%e8%9b%8b%e7%99%bd%e5%ba%8f%e5%88%97%e6%af%94%e5%af%b9%e5%88%b0nr%e6%95%b0%e6%8d%ae%e5%ba%93","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2703","title":{"rendered":"\u4f7f\u7528DIAMOND\u5c06\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\u6bd4\u5bf9\u5230Nr\u6570\u636e\u5e93"},"content":{"rendered":"

1. DIAMOND<\/a>\u7b80\u4ecb<\/h1>\n

\u5bf9\u5168\u57fa\u56e0\u7ec4\u7684\u57fa\u56e0\u8fdb\u884cNr\u6ce8\u91ca\u662f\u5fc5\u4e0d\u53ef\u5c11\u7684\u4e00\u6b65\u3002\u7531\u4e8eNr\u6570\u636e\u5e93\u975e\u5e38\u5927\uff0c\u5bfc\u81f4\u4f7f\u7528BLAST\u4f1a\u6d88\u8017\u5de8\u5927\u7684\u8ba1\u7b97\u8d44\u6e90\u548c\u65f6\u95f4\u3002\u4f7f\u7528DIAMOND<\/a>\u5219\u80fd\u5feb500-20000\u500d\uff0c\u800c\u83b7\u5f97\u548cBLAST\u6bd4\u8f83\u4e00\u81f4\u7684\u7ed3\u679c\u3002\u7279\u522b\u662f\u5bf9\u4e8e\u957f\u5ea6\u4e3a100-150bp\uff0c\u6570\u91cf\u8d85\u8fc71M\u7684\u6838\u9178\u5e8f\u5217\uff0cDIAMOND\u7684\u901f\u5ea6\u6bd4BLASTX\u5feb20000\u500d\uff1b\u5f53e-value\u8bbe\u7f6e\u4e3a1e-5\u65f6\uff0cDIAMOND\u80fd\u62a5\u544a80~90%\u7684BLASTX\u5339\u914d\u7ed3\u679c\uff1b\u82e5\u8bbe\u7f6esensitivie\u6a21\u5f0f\uff0cDIAMOND\u901f\u5ea6\u662fBLASTX\u76842500\u500d\uff0cDIAMOND\u80fd\u62a5\u544a94%\u7684BLASTX\u5339\u914d\u7ed3\u679c\u3002\u56e0\u6b64\uff0c\u5bf9\u5927\u6279\u91cf\u7684\u5e8f\u5217\u8fdb\u884cNr\u6ce8\u91ca\u6216\u89c4\u6a21\u8f83\u5927\u7684\u86cb\u767d\u6570\u636e\u5e93\u7684\u6bd4\u5bf9\uff0c\u4f7f\u7528DIAMOND\u662f\u4f18\u5148\u9009\u62e9\u7684\u65b9\u5f0f\u3002<\/p>\n

\u867d\u7136DIAMOND\u8f6f\u4ef6\u7684\u8fd0\u884c\u901f\u5ea6\u5feb\uff0c\u4f46\u662f\u5176\u7ed3\u679c\u4e2d\u6ca1\u6709\u5339\u914d\u7684Subject\u5e8f\u5217\u7684\u63cf\u8ff0\u4fe1\u606f\u3002\u82e5\u9700\u8981\u86cb\u767d\u540d\u79f0\u548c\u7269\u79cd\u7684\u63cf\u8ff0\u4fe1\u606f\uff0c\u9700\u8981\u81ea\u884c\u7f16\u5199\u8f6f\u4ef6\u4ece\u6570\u636e\u5e93\u7684FASTA\u6587\u4ef6\u4e2d\u63d0\u53d6\u5e76\u6574\u5408\u5230DIAMOND\u7ed3\u679c\u4e2d\u3002<\/p>\n

2. DIAMOND\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n
$ wget https:\/\/github.com\/bbuchfink\/diamond\/releases\/download\/v0.9.24\/diamond-linux64.tar.gz -P ~\/software\/\n$ mkdir \/opt\/biosoft\/diamond\n$ tar zxf ~\/software\/diamond-linux64.tar.gz -C \/opt\/biosoft\/diamond\n$ echo 'PATH=$PATH:\/opt\/biosoft\/diamond' >> ~\/.bashrc\n$ source ~\/.bashrc\n<\/pre>\n
3. DIAMOND\u4f7f\u7528<\/a><\/h1>\n
DIAMOND\u8f6f\u4ef6\u7684\u4e3b\u547d\u4ee4\u662fdiamond\uff0c\u5b83\u7684\u4f7f\u7528\u5305\u542b\u51e0\u4e2a\u5b50\u547d\u4ee4\u3002DIAMOND\u6700\u5e38\u7528\u7684\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n
\u4f7f\u7528DIAMOND\u8f6f\u4ef6\u7684\u5b50\u547d\u4ee4makedb\u5c06FASTA\u683c\u5f0f\u7684\u86cb\u767d\u5e8f\u5217\u521b\u5efa\u6210\u540e\u7f00\u4e3admnd\u7684\u6570\u636e\u5e93\u6587\u4ef6\uff1a\n$ diamond makedb --in nr_eukaryon.fasta -d nr_eukaryon_20190405\n    \u5c06Nr\u6570\u636e\u5e93\uff08\u7248\u672c20190405\uff09\u7684\u771f\u6838\u5b50\u96c6\u521b\u5efa\u6210DIAMOND\u6570\u636e\u5e93\uff0c\u6570\u636e\u5e93\u5305\u542b37.4M\u6761\u86cb\u767d\u5e8f\u5217\uff0c\u670d\u52a1\u5668\u662f24\u7ebf\u7a0b2.0GHz\u7684CPU\u8d44\u6e90\uff0c\u8017\u65f617min\u3002\n\n\u5c06Illumina\u6d4b\u5e8f\u6570\u636e\u6bd4\u5bf9\u5230\u6570\u636e\u5e93\uff1a\n$ diamond blastx --db nr_eukaryon_20190405 --query reads.fq.gz --out reads.tab\n\n\u5c06\u5168\u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\u6bd4\u5bf9\u5230\u6570\u636e\u5e93\uff1a\n$ diamond blastp --db nr_eukaryon_20190405 --query proteins.fasta --out nr.tab --outfmt 6 --sensitive --max-target-seqs 20 --evalue 1e-5 --id 30 --block-size 20.0 --tmpdir \/dev\/shm --index-chunks 1\n    \u5bf918700\u4e2a\u86cb\u767d\u5e8f\u5217\u8fdb\u884cNr\u6ce8\u91ca\uff0c\u670d\u52a1\u5668160\u7ebf\u7a0b2.4GHz\u7684CPU\u8d44\u6e90\uff0c\u8017\u65f691min\uff08\u4e0d\u52a0--sensitive\u53c2\u6570\u53ea\u9700\u898116min\uff09\u3002\n<\/pre>\n
\u6b64\u5916\uff0cDIAMOND\u8fd8\u5305\u542b\u5176\u5b83\u51e0\u4e2a\u5b50\u547d\u4ee4\uff1a<\/p>\n
blastx\n    \u5c06\u6838\u9178\u5e8f\u5217\u6bd4\u5bf9\u5230\u86cb\u767d\u5e8f\u5217\u6570\u636e\u5e93\nview\n    \u4eceDAA\u6587\u4ef6\u751f\u6210\u683c\u5f0f\u5316\u7684\u8f93\u51fa\u7ed3\u679c\ngetseq\n    \u4eceDIAMOND\u6570\u636e\u5e93\u6587\u4ef6\u83b7\u53d6FASTA\u5e8f\u5217\nversion\n    \u6253\u5370DIAMOND\u8f6f\u4ef6\u7684\u7248\u672c\u53f7\ndbinfo\n    \u6253\u5370\u6570\u636e\u5e93\u7684\u4fe1\u606f\nhelp\n    \u6253\u5370DIAMOND\u8f6f\u4ef6\u7684\u8be6\u7ec6\u5e2e\u52a9\u4fe1\u606f<\/pre>\n
DIAMOND\u7684\u53c2\u6570\uff1a<\/p>\n
\u6570\u636e\u5e93\u53c2\u6570\uff1a<\/strong>\n--in <string>    default: STDIN\n    \u8f93\u5165FASTA\u683c\u5f0f\u7684\u86cb\u767d\u5e8f\u5217\u6570\u636e\u5e93\u6587\u4ef6\u3002\n--db | -d <string>\n    \u8bbe\u7f6e\u6570\u636e\u5e93\u6587\u4ef6\u8def\u5f84\u548c\u524d\u7f00\u3002\u521b\u5efa\u6570\u636e\u5e93\u65f6\uff0c\u4f1a\u751f\u6210\u4e00\u4e2a\u540e\u7f00\u4e3a.dmnd\u7684\u6570\u636e\u5e93\u6587\u4ef6\u3002\u6bd4\u5bf9\u65f6\uff0c\u5219\u662f\u8f93\u5165\u76f8\u5e94\u7684\u6570\u636e\u5e93\u6587\u4ef6\u3002\n--taxonmap <string>\n--taxonnodes <string>\n    \u8fd9\u4e24\u4e2a\u53c2\u6570\u8f93\u5165NCBI\u7684\u7269\u79cd\u5206\u7c7b\u4fe1\u606f\u3002\u524d\u8005\u8f93\u5165Nr\u6570\u636e\u5e93\u4e2d\u86cb\u767d\u7f16\u53f7\u548c\u7269\u79cd\u7f16\u53f7\u7684\u5bf9\u5e94\u5173\u7cfb\u4fe1\u606f\uff08 ftp:\/\/ftp.ncbi.nlm.nih.gov\/pub\/taxonomy\/accession2taxid\/prot.accession2taxid.gz\uff09\uff1b\u540e\u8005\u8f93\u5165\u7269\u79cd\u7f16\u53f7\u7684\u5c42\u6b21\u4fe1\u606f\uff08ftp:\/\/ftp.ncbi.nlm.nih.gov\/pub\/taxonomy\/taxdmp.zip\uff09\u3002\u8f93\u5165\u8fd9\u4e24\u4e2a\u6587\u4ef6\u6709\u5229\u4e8eDIAMOND\u548cNr\u6570\u636e\u5e93\u8fdb\u884c\u6bd4\u5bf9\u65f6\uff0c\u53ef\u4ee5\u9009\u62e9\u548c\u6570\u636e\u5e93\u4e2d\u6307\u5b9a\u7684\u7269\u79cd\u5927\u7c7b\u7684\u6570\u636e\u8fdb\u884c\u6bd4\u5bf9\u3002\n\n\u8f93\u5165\u53c2\u6570\uff1a<\/strong>\n--db | -d <string>\n    \u8bbe\u7f6e\u6570\u636e\u5e93\u6587\u4ef6\u8def\u5f84\u548c\u524d\u7f00\u3002\u521b\u5efa\u6570\u636e\u5e93\u65f6\uff0c\u4f1a\u751f\u6210\u4e00\u4e2a\u540e\u7f00\u4e3a.dmnd\u7684\u6570\u636e\u5e93\u6587\u4ef6\u3002\u6bd4\u5bf9\u65f6\uff0c\u5219\u662f\u8f93\u5165\u76f8\u5e94\u7684\u6570\u636e\u5e93\u6587\u4ef6\u3002\n--query | -q <string>    default: STDIN\n    \u8f93\u5165\u9700\u8981\u6ce8\u91ca\u7684FASTA\u6216FASTQ\u683c\u5f0f\u7684\u5e8f\u5217\u6587\u4ef6\u3002\u53ef\u4ee5\u662f\u5e26.gz\u540e\u7f00\u7684\u538b\u7f29\u6587\u4ef6\u3002\n--taxonlist <string>\n    \u8f93\u5165NCBI\u5206\u7c7b\u7f16\u53f7\uff0c\u4ec5\u5bf9\u6570\u636e\u5e93\u4e2d\u7684\u76ee\u6807\u5b50\u96c6\u8fdb\u884c\u6bd4\u5bf9\u3002\u53ef\u4ee5\u8f93\u5165\u591a\u4e2a\u4f7f\u7528\u9017\u53f7\u5206\u9694\u7684\u7f16\u53f7ID\u3002\u4f8b\u5982\uff0c\u53e4\u83cc(2157)\u3001\u7ec6\u83cc(2)\u3001\u75c5\u6bd2(10239)\u3001\u771f\u83cc\uff084751\uff09\u3001\u52a8\u7269\uff0833208\uff09\u548c\u690d\u7269\uff083193\uff09\u3002\u4f7f\u7528\u8be5\u53c2\u6570\uff0c\u5fc5\u987b\u8981\u4f7f\u7528--taxonmap\u548c--taxonnodes\u53c2\u6570\u6784\u5efa\u6570\u636e\u5e93\u3002\n--query-gencode <int>    default\uff1a1\n    \u8bbe\u7f6e\u5728\u8fdb\u884cBLASTX\u6a21\u5f0f\u8fdb\u884c\u6bd4\u5bf9\u65f6\u6240\u4f7f\u7528\u7684\u9057\u4f20\u5bc6\u7801<\/a>\u3002\n--strand <string>    default: both\n    \u8bbe\u7f6e\u5bf9query\u5e8f\u5217\u7684\u90a3\u6761\u94fe\u8fdb\u884c\u6bd4\u5bf9\u3002\u53ef\u4ee5\u8bbe\u7f6e\u7684\u503c\u4e3a\uff1aboh\u3001plus\u548cminus\u3002\n--min-orf | -l <int>\n    \u5728\u4f7f\u7528BLASTX\u6a21\u5f0f\u8fdb\u884c\u6bd4\u5bf9\u65f6\uff0c\u82e5\u5e8f\u5217\u7684\u67d0\u4e2aORF\u4f4e\u4e8e\u6b64\u503c\uff0c\u5219\u5ffd\u7565\u8be5ORF\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff1a\u82e5\u6838\u9178\u5e8f\u5217\u957f\u5ea6\u4f4e\u4e8e30\uff0c\u5219\u503c\u4e3a1\uff1b\u82e5\u6838\u9178\u5e8f\u5217\u957f\u5ea6\u4f4e\u4e8e100\uff0c\u5219\u503c\u4e3a20\uff1b\u82e5\u6838\u9178\u5e8f\u5217\u957f\u5ea6\u4e0d\u4f4e\u4e8e100\uff0c\u5219\u503c\u4e3a40\u3002\u82e5\u8be5\u503c\u8bbe\u4e3a1\uff0c\u5219\u8868\u793a\u5728BLASTX\u6a21\u5f0f\u65f6\uff0c\u8bc6\u522b\u6240\u6709\u957f\u5ea6\u7684ORF\u5e76\u8fdb\u884c\u6bd4\u5bf9\u3002\n\n\u6bd4\u5bf9\u53c2\u6570\uff1a<\/strong>\n--sensitive\n    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u5219\u80fd\u5f97\u5230\u66f4\u591a\u6bd4\u5bf9\u7ed3\u679c\u3002\u8be5\u6a21\u5f0f\u9002\u5408\u6bd4\u5bf9\u8f83\u957f\u7684\u5e8f\u5217\u3002\u9ed8\u8ba4\u6a21\u5f0f\u4e3b\u8981\u9002\u7528\u4e8e\u6bd4\u5bf9short reads\u5e8f\u5217\uff08Illumina reads\uff09\uff0c\u641c\u5bfb\u6bd4\u5bf9\u957f\u5ea6\u4e3a30~40aa\u4e14bit\u5f97\u5206\u5927\u4e8e50\u7684\u5339\u914d\u7ed3\u679c\u3002\n--more-sensitive\n    \u76f8\u6bd4\u4e8esensitive\uff0c\u80fd\u5f97\u5230\u66f4\u5168\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\n--frameshifit | -F <int>\n    \u5728\u8fdb\u884cBLASTX\u6a21\u5f0f\u65f6\uff0c\u8bbe\u7f6e\u5bf9\u79fb\u7801\u5339\u914d\u7684\u7f5a\u5206\uff0c\u4e14\u4e00\u822c\u63a8\u8350\u8bbe\u7f6e\u8be5\u53c2\u6570\u503c\u4e3a15\u5de6\u53f3\u3002\u8bbe\u7f6e\u8be5\u53c2\u6570\u540e\uff0c\u6709\u5229\u4e8e\u6bd4\u5bf9\u8f83\u957f\u7684\u6709INDEL\u9519\u8bef\u7684reads\u5e8f\u5217\u3002\u9ed8\u8ba4\u60c5\u51b5\u662f\u662f\u7981\u7528\u4e86\u6b64\u529f\u80fd\u3002\n--gapopen <int>    default: BLOSUM62\u77e9\u9635\u7684\u9ed8\u8ba4\u503c\u4e3a1\n    \u8bbe\u7f6e\u6253\u5f00Gap\u7f5a\u5206\u3002\n--gapextend <int>    default: BLOSUM62\u77e9\u9635\u7684\u9ed8\u8ba4\u503c\u4e3a1\n    \u8bbe\u7f6e\u5ef6\u957fGap\u7f5a\u5206\u3002\n--matrix <string>    default: BLOSUM62\n    \u8bbe\u7f6e\u8ba1\u5206\u77e9\u9635\u3002\u53ef\u4ee5\u8bbe\u7f6e\u7684\u503c\u6709\uff1aBLOSUM45\uff0cBLOSUM50\uff0cBLOSUM62\uff0cBLOSUM80\uff0cBLOSUM90\uff0cPAM250\uff0cPAM70\u548cPAM30\u3002\n--comp-based-stats <bool>    default: 1\n    \u8bbe\u7f6e\u662f\u5426\u5bf9\u6bd4\u5bf9\u5f97\u5206\u8fdb\u884c\u6821\u6b63\u3002\n--algo <bool>\n    \u8bbe\u7f6e\u79cd\u5b50\u5e8f\u5217\u641c\u7d22\u7684\u7b97\u6cd5\u30020\u8868\u793a\u4f7f\u7528double-indexed\u7b97\u6cd5\uff0c1\u8868\u793aquery-indexed\u7b97\u6cd5\u3002\u7b2c\u4e00\u79cd\u7b97\u6cd5\u662f\u8f6f\u4ef6\u7684\u4e3b\u8981\u7b97\u6cd5\uff0c\u4f46\u4e0d\u9002\u5408query\u6570\u636e\u8f83\u5c11\u7684\u60c5\u51b5\uff0c\u8fd9\u65f6\u9700\u8981\u4f7f\u7528\u7b2c\u4e8c\u79cd\u7b97\u6cd5\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0c\u8f6f\u4ef6\u4f1a\u6839\u636equery\u548c\u6570\u636e\u5e93\u7684\u6570\u636e\u91cf\u81ea\u52a8\u9009\u62e9\u76f8\u5e94\u7684\u7b97\u6cd5\u3002\u4e24\u79cd\u7b97\u6cd5\u7684\u7ed3\u679c\u57fa\u672c\u4e00\u81f4\u3002\n--freq-sd <int>\n    \u8bbe\u7f6e\u79cd\u5b50\u5e8f\u5217\u6700\u5927\u7684\u5339\u914d\u9891\u7387\u3002\u82e5\u79cd\u5b50\u5e8f\u5217\u5728query\u6216\u6570\u636e\u5e93\u79cd\u51fa\u73b0\u7684\u9891\u7387\u8fc7\u9ad8\uff0c\u5219\u5ffd\u7565\u4e4b\u3002\u5728\u4e00\u822c\u6a21\u5f0f\u4e0b\uff0c\u8be5\u53c2\u6570\u503c\u4e3a50\uff1b\u5728sensitive\u6a21\u5f0f\u4e0b\uff0c\u8be5\u53c2\u6570\u503c\u4e3a100\uff0c\u5728more-sensitive\u6a21\u5f0f\u4e0b\uff0c\u8be5\u53c2\u6570\u503c\u4e3a200\u3002\n\n\n\u8f93\u51fa\u53c2\u6570\uff1a<\/strong>\n--out | -o <string>    default\uff1aSTDOUT\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u3002\n--outfmt | -f <int>    default: 6\n    \u8bbe\u7f6e\u8f93\u51fa\u683c\u5f0f\u3002\u652f\u6301\u7684\u683c\u5f0f\u6709\uff1a0\uff0c\u4e24\u4e24\u6bd4\u5bf9\u683c\u5f0f\uff1b5\uff0cXML\u683c\u5f0f\uff1b6\uff0cBLAST\u8868\u683c\u683c\u5f0f\uff1b100\uff0cDIAMOND\u5339\u914d\u5b58\u6863\uff08DDA\uff09\u683c\u5f0f\uff0c\u8be5\u683c\u5f0f\u53ef\u4ee5\u4f7f\u7528diamond view\u547d\u4ee4\u8f6c\u6362\u6210\u5176\u5b83\u683c\u5f0f\uff1b101\uff0cSAM\u683c\u5f0f\uff1b102\uff0c\u5206\u7c7b\u9274\u5b9a\u7ed3\u679c\uff0c\u8be5\u6a21\u5f0f\u4e0b\u7ed3\u679c\u6587\u4ef6\u5206\u4e09\u5217\uff0cQueryID\u3001NCBI\u7269\u79cd\u5206\u7c7bID\u3001\u6700\u4f73\u5339\u914devaule\uff1b103\uff0cPAF\u683c\u5f0f\u3002\n--salltitles\n    \u5728DDA\u683c\u5f0f\u7ed3\u679c\u4e2d\u5305\u542ball subject titles\u3002\n--sallseqid\n    \u5728DDA\u683c\u5f0f\u7ed3\u679c\u4e2d\u5305\u542ball subject ids\u3002\u7531\u4e8eid\u6bd4title\u8981\u77ed\uff0c\u76f8\u6bd4\u4e8e--salltitles\uff0c\u672c\u53c2\u6570\u8f93\u51fa\u7684\u7ed3\u679c\u6587\u4ef6\u66f4\u5c0f\u3002\n--compress <bool>    default: 0\n    \u8bbe\u7f6e\u662f\u5426\u5bf9\u6691\u4fc3\u6587\u4ef6\u8fdb\u884c\u538b\u7f29\u30020\u8868\u793a\u4e0d\u538b\u7f29\uff0c1\u8868\u793a\u8fdb\u884cgzip\u538b\u7f29\u3002\n--max-target-seqs | -k <int>    default: 25\n    \u8bbe\u7f6e\u6bcf\u4e2aquery\u6bd4\u5bf9\u7ed3\u679c\u7684\u6700\u5927\u5339\u914d\u6570\u76ee\u3002\n--top <int>\n    \u82e5\u8bbe\u7f6e\u8be5\u53c2\u6570\u7684\u503c\uff0c\u5219\u62a5\u544a\u4e00\u5b9a\u6570\u76ee\u7684top\u5339\u914d\u7ed3\u679c\u3002\u4f8b\u5982\u8bbe\u7f6e\u8be5\u53c2\u6570\u503c\u4e3a10\uff0c\u5219\u62a5\u544a\u5339\u914d\u5f97\u5206\u4e3atop10\u7684\u7ed3\u679c\uff0c\u5373\u62a5\u544a\u6240\u6709\u5f97\u5206\u548c\u6700\u9ad8\u5f97\u5206\u76f8\u5dee10%\u4ee5\u5185\u7684\u5339\u914d\u7ed3\u679c\u3002\u8be5\u53c2\u6570\u4f1a\u53d6\u4ee3--max-target-seqs\u53c2\u6570\u8bbe\u7f6e\u7684\u503c\u3002\n--range-culling\n    \u6dfb\u52a0\u8be5\u53c2\u6570\u80fd\u5254\u9664\u5339\u914d\u5230query\u5e8f\u5217\u76f8\u540c\u4f4d\u7f6e\u7684hit\u7ed3\u679c\u3002\u8be5\u53c2\u6570\u9002\u5408\u4e8e\u8f83\u957f\u7684query DNA\u5e8f\u5217\u3002\u5f53DNA\u5e8f\u5217\u8f83\u957f\u65f6\uff0c\u5b83\u53ef\u80fd\u8de8\u8d8a\u591a\u4e2a\u57fa\u56e0\uff0c\u800c\u4e00\u822c\u60c5\u51b5\u4e0b\u4ec5\u62a5\u544a25\u4e2a\u6700\u4f73\u5339\u914d\u7ed3\u679c\uff0c\u82e5\u8fd925\u4e2ahits\u7ed3\u679c\u53ef\u80fdevaule\u503c\u5f88\u597d\u4f46\u5f97\u5206\u8f83\u4f4e\uff0c\u4e14\u4e00\u8d77\u4e0d\u80fd\u8986\u76d6query\u5e8f\u5217\u768450%\uff0c\u4f1a\u5bfc\u81f4\u9635\u52bf\u7684\u6bd4\u5bf9\u7ed3\u679c\u8f83\u5dee\u3002\u56e0\u6b64\uff0c\u6dfb\u52a0\u8be5\u53c2\u6570\u80fd\u5254\u9664\u5339\u914d\u5230query\u5e8f\u5217\u76f8\u540c\u4f4d\u7f6e\u7684hit\u7ed3\u679c\uff0c\u4ee5\u4f7f\u6700\u7ec8\u7684\u6bd4\u5bf9\u7ed3\u679c\u5bf9query\u5e8f\u5217\u7684\u8986\u76d6\u7387\u8d85\u8fc750%\u3002\n--range-cover <float>    default: 50.0\n    \u548c\u53c2\u6570--range-culling\u914d\u5408\u4f7f\u7528\uff0c\u8868\u793a\u5254\u9664hits\u4ee5\u4f7f\u6240\u6709\u7684\u6bd4\u5bf9\u7ed3\u679c\u80fd\u5bf9query\u5e8f\u5217\u7684\u8986\u76d6\u7387\u8d85\u8fc7\u6b64\u53c2\u6570\u8bbe\u5b9a\u7684\u767e\u5206\u6bd4\u3002\n--long-reads\n    \u5bf9\u4e8elong read DNA\u6d4b\u5e8f\u6570\u636e\uff0c\u63a8\u8350\u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u7b49\u540c\u53c2\u6570--range-culling --top 10 -F 15\u3002\n--evalue | -e <float>    default: 0.001\n    \u8bbe\u7f6e\u6bd4\u5bf9\u7684evalue\u9608\u503c\u3002\n--min-score <int>\n    \u8bbe\u7f6e\u6bd4\u5bf9\u7684bit score\u9608\u503c\u3002\u8bbe\u7f6e\u8be5\u53c2\u6570\u4f1a\u66ff\u4ee3--evalue\u53c2\u6570\u3002\n--id <int>\n    \u8bbe\u7f6eidentity\u9608\u503c\u3002\n--query-cover <int>\n    \u8bbe\u7f6e\u5bf9query\u5e8f\u5217\u7684\u8986\u76d6\u5ea6\u9608\u503c\u3002\u8be5\u9608\u503c\u662fHSP\u7684\u9608\u503c\u3002\n--subject-cover <int>\n    \u8bbe\u7f6e\u5bf9subject\u5e8f\u5217\u7684\u8986\u76d6\u5ea6\u9608\u503c\u3002\u8be5\u9608\u503c\u662fHSP\u7684\u9608\u503c\u3002\n--max-hsps <int>\n    \u8bbe\u7f6e\u62a5\u544a\u7684HSPs\u6570\u91cf\u3002\u9ed8\u8ba4\u662f\u62a5\u544a\u6240\u6709\u7684HSPs\uff0c\u82e5\u8bbe\u7f6e\u62101\uff0c\u5219\u4ec5\u62a5\u544a\u6700\u4f18HSP\u3002\n--unal <bool>\n    \u8bbe\u7f6e\u662f\u5426\u62a5\u544a\u6ca1\u6709\u5339\u914d\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0c--outfmt\u4e3a1\u30015\u548c101\u65f6\uff0c\u8be5\u53c2\u6570\u503c\u4e3a1\uff0c\u5176\u5b83\u8f93\u51fa\u65b9\u5f0f\u8be5\u53c2\u6570\u503c\u4e3a0\u3002\n--no-self-hits\n    \u6dfb\u52a0\u8be5\u53c2\u6570\uff0c\u5219\u4e0d\u62a5\u544a\u5e8f\u5217\u548c\u81ea\u5df1\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\n\n\u6027\u80fd\u53c2\u6570\uff1a<\/strong>\n--threads | -p <int>    default: Max\n    \u8bbe\u7f6e\u7a0b\u5e8f\u8fd0\u884c\u6240\u4f7f\u7528\u7684CPU\u7ebf\u7a0b\u6570\u3002\u9ed8\u8ba4\u662f\u670d\u52a1\u5668\u53ef\u7528\u7684\u6700\u5927CPU\u7ebf\u7a0b\u6570\u3002\n--block-size | -b <float>    default: 2.0\n    \u8bbe\u7f6e\u6bcf\u6b21\u5904\u7406\u591a\u5c11G\u7684\u5e8f\u5217\u5b57\u7b26\u6570\u3002\u8be5\u53c2\u6570\u63a7\u5236\u7a0b\u5e8f\u6d88\u8017\u7684\u5185\u5b58\u91cf\uff0c\u4e00\u822c\u5185\u5b58\u6d88\u8017\u8be5\u503c\u76846\u500d\u3002\u8bbe\u7f6e\u66f4\u5927\u7684\u503c\uff0c\u4f1a\u6d88\u8017\u66f4\u591a\u7684\u5185\u5b58\u548c\u4e34\u65f6\u78c1\u76d8\u7a7a\u95f4\uff0c\u4f46\u80fd\u63d0\u9ad8\u6027\u80fd\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0c\u7a0b\u5e8f\u4e00\u6b21\u5904\u74062G\u4e2a\u5e8f\u5217\u5b57\u7b26\uff0c\u6d88\u8017\u5185\u5b5812G\u3002\n--tmpdir | -t <string>    default: directory of --out\n    \u8bbe\u7f6e\u4e34\u65f6\u6587\u4ef6\u5939\u8def\u5f84\u3002\u63a8\u8350\u8be5\u6587\u4ef6\u6240\u5728\u5269\u4f59\u78c1\u76d8\u7a7a\u95f4\u6709100G\u53ca\u4ee5\u4e0a\u3002\u82e5\u5c06\u8be5\u53c2\u6570\u8bbe\u7f6e\u4e3a\/dev\/shm\uff0c\u5219\u4f1a\u5c06\u4e34\u65f6\u6587\u4ef6\u5b58\u653e\u5728\u5185\u5b58\uff0c\u4f1a\u589e\u52a0\u5185\u5b58\u6d88\u8017\u548c\u8ba1\u7b97\u6027\u80fd\u3002\n--index-chunks | -c <int>    default: 4\n    \u5c06seed index\u5206\u6210\u6307\u5b9a\u7684\u4efd\u6570\u3002\u63a8\u8350\u5c06\u8be5\u53c2\u6570\u503c\u8bbe\u7f6e\u62101\uff0c\u80fd\u589e\u52a0\u8ba1\u7b97\u6027\u80fd\u548c\u5185\u5b58\u4f7f\u7528\u91cf\u3002\n<\/pre>\n\n\n
DIAMOND\u8f6f\u4ef6\u8fd0\u884c\u8fc7\u7a0b\u4e2d\uff0c\u82e5\u4f7f\u7528\u53c2\u6570 –block-size 20.0 –tmpdir \/dev\/shm –index-chunks 1 \u80fd\u4f7f\u7528\u8f83\u5927\u5185\u5b58\uff0c\u4e0d\u4f1a\u5bf9\u6570\u636e\u8fdb\u884c\u5206\u5757\uff0c\u7a0b\u5e8f\u8fd0\u884c\u8f83\u5feb\u3002\u7a0b\u5e8f\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u53ef\u80fd\u5b8c\u5168\u4e0d\u4f1a\u751f\u6210\u8fc7\u7a0b\u6587\u4ef6\u3002\u4f46\u5728\u7a0b\u5e8f\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u7ed9\u51fa\u4e00\u4e9b\u8fdb\u5ea6\u4fe1\u606f\u3002\u5f53shape\u523015\u7684\u65f6\u5019\uff0c\u5219\u8868\u793a\u7a0b\u5e8f\u5feb\u8fd0\u884c\u5b8c\u6bd5\u3002\u901a\u8fc7\u67e5\u770bshape\u503c\u6765\u786e\u5b9a\u7a0b\u5e8f\u8fd0\u884c\u7684\u8fdb\u5ea6\u3002<\/p>\n\n\n\n
CPU threads: 160
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11\/1)
Temporary directory: \/dev\/shm
Opening the database\u2026
Target sequences to report alignments for: 20
Opening the input file\u2026
Opening the output file\u2026
Loading query sequences\u2026
Masking queries\u2026
Building query seed set\u2026
Algorithm: Double-indexed
Building query histograms\u2026
Allocating buffers\u2026
Loading reference sequences\u2026
Building reference histograms\u2026
Allocating buffers\u2026
Initializing temporary storage\u2026
Processing query chunk 0, reference chunk 0, shape 0, index chunk 0.
Building reference index\u2026
Building query index\u2026
Building seed filter\u2026
Searching alignments\u2026 
Processing query chunk 0, reference chunk 0, shape 1, index chunk 0.
Building reference index\u2026
Building query index\u2026
Building seed filter\u2026
Searching alignments\u2026 
...
Processing query chunk 0, reference chunk 0, shape 15, index chunk 0.
Building reference index\u2026
Building query index\u2026
Building seed filter\u2026
Searching alignments\u2026
Deallocating buffers\u2026
Computing alignments\u2026
Deallocating reference\u2026
Loading reference sequences\u2026
Deallocating buffers\u2026
Deallocating queries\u2026
Loading query sequences\u2026
Closing the input file\u2026
Closing the output file\u2026
Closing the database file\u2026
Deallocating taxonomy\u2026
Total time = 659.515s
Reported 33888205 pairwise alignments, 33890340 HSPs.
122518 queries aligned.
<\/pre>\n\n\n\n
DIAMOND\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\u8f93\u51fa\u8868\u683c\u683c\u5f0f\u7684\u7ed3\u679c\u3002\u7ed3\u679c\u520612\u5217\uff0c\u5176\u7ed3\u679c\u4fe1\u606f\u548cBLAST\u9ed8\u8ba4\u8bbe\u7f6e-outfmt 6\u8f93\u51fa\u7684\u683c\u5f0f\u5b8c\u5168\u4e00\u81f4\u3002<\/p>\n\n\n\n
1. query\u5e8f\u5217ID
2. subject\u5e8f\u5217ID
3. Identity\u767e\u5206\u6bd4
4. \u5339\u914d\u957f\u5ea6
5. \u9519\u914d\u957f\u5ea6
6. \u6253\u5f00Gap\u7684\u6b21\u6570
7. query\u5e8f\u5217\u8d77\u59cb\u4f4d\u70b9
8. query\u5e8f\u5217\u7ed3\u675f\u4f4d\u70b9
9. subject\u5e8f\u5217\u8d77\u59cb\u4f4d\u70b9
10. subject\u5e8f\u5217\u7ed3\u675f\u4f4d\u70b9
11. E-vaule\u503c
12. bitscore\u5f97\u5206<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. DIAMOND\u7b80\u4ecb \u5bf9\u5168\u57fa\u56e0\u7ec4\u7684\u57fa\u56e0\u8fdb\u884cNr\u6ce8\u91ca\u662f\u5fc5\u4e0d\u53ef\u5c11\u7684\u4e00\u6b65\u3002\u7531\u4e8eNr … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2703"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2703"}],"version-history":[{"count":15,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2703\/revisions"}],"predecessor-version":[{"id":2773,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2703\/revisions\/2773"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2703"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2703"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2703"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}