{"id":2465,"date":"2017-04-16T22:48:09","date_gmt":"2017-04-16T14:48:09","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2465"},"modified":"2017-04-18T01:16:16","modified_gmt":"2017-04-17T17:16:16","slug":"falcon","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2465","title":{"rendered":"FALCON"},"content":{"rendered":"<h1>1. \u5b89\u88c5FALCON<\/h1>\n<pre>\r\n$ cd \/opt\/biosoft\r\n$ export GIT_SYM_CACHE_DIR=~\/.git-sym-cache # to speed things up\r\n$ git clone git:\/\/github.com\/PacificBiosciences\/FALCON-integrate.git\r\n$ cd FALCON-integrate\r\n$ git checkout master  # or whatever version you want\r\n$ git submodule update --init # Note: You must do this yourself! No longer via `make init`.\r\n$ make init\r\n$ source env.sh\r\n$ make config-edit-user\r\n$ make -j all\r\n$ make test  # to run a simple one\r\n<\/pre>\n<h1>2. FALCON\u8fd0\u884c\u793a\u4f8b<\/h1>\n<pre>\r\n\u5148\u8bbe\u7f6e\u597d\u73af\u5883\u53d8\u91cf\r\n$ cd \/opt\/biosoft\/FALCON-integrate\/\r\n$ source env.sh\r\n\r\n\u4e0b\u8f7d\u57fa\u56e0\u7ec4\u5927\u5c0f\u53ea\u6709200kb\u7684greg200k\u6570\u636e\uff0c\u4ee5\u53ca\u57fa\u56e0\u7ec4\u5927\u5c0f\u67094.6Mb\u7684E. coli\u6570\u636e\r\n$ cd FALCON-examples\/.git-sym\/\r\n$ curl -L https:\/\/downloads.pacbcloud.com\/public\/data\/git-sym\/greg200k-sv2.tar | tar xvf -\r\n$ curl -L https:\/\/downloads.pacbcloud.com\/public\/data\/git-sym\/ecoli.m140913_050931_42139_c100713652400000001823152404301535_s1_p0.subreads.tar | tar xvf -\r\n\r\n\u5bf9200kb\u57fa\u56e0\u7ec4\u8fdb\u884c\u7ec4\u88c5\r\n$ cd \/opt\/biosoft\/FALCON-integrate\/FALCON-examples\/run\/greg200k-sv2\r\n$ fc_run.py fc_run.cfg\r\n\r\n\u5bf94.6Mb\u57fa\u56e0\u7ec4\u8fdb\u884c\u7ec4\u88c5\r\n$ cd \/opt\/biosoft\/FALCON-integrate\/FALCON-examples\/run\/ecoli\r\n$ perl -p -i -e 's\/^#job_type\/job_type\/' fc_run.cfg\r\n$ fc_run.py fc_run.cfg\r\n\r\n\u751f\u6210\u7684\u6700\u7ec8\u7ed3\u679c\u6587\u4ef6\u4e3a 2-asm-falcon\/p_ctg.fa \u3002\r\n<\/pre>\n<h1>3. <a href=\"https:\/\/github.com\/PacificBiosciences\/FALCON\/wiki\/Manual\" target=\"_blank\">FALCON\u5de5\u4f5c\u539f\u7406<\/a><\/h1>\n<pre>\r\n1. \u5bf9\u539f\u59cbsubreads\u8fdb\u884cOverlapping\u5206\u6790\r\n2. \u8fdb\u884c\u9884\u7ec4\u88c5\uff0c\u5bf9Subreads\u8fdb\u884c\u6821\u6b63\r\n3. \u5bf9\u6821\u6b63\u540e\u7684Subreads\u8fdb\u884cOverlapping\u5206\u6790\r\n4. \u8fc7\u6ee4\u4e0d\u53ef\u9760\u7684Overlaps\u7ed3\u679c\r\n5. \u6839\u636e\u53ef\u9760\u7684Overlap\u6784\u5efaGrahp\r\n6. \u7531Grahp\u5f97\u5230contigs\u5e8f\u5217\r\n<\/pre>\n<h1>4. FALCON\u7684\u914d\u7f6e\u6587\u4ef6<\/h1>\n<p>FALCON\u8f6f\u4ef6\u7684\u8f93\u5165\u6587\u4ef6\u662fPacbio\u6d4b\u5e8f\u5f97\u5230\u7684Fasta\u6587\u4ef6\u3002\u5c06\u8fd9\u4e9bFasta\u6587\u4ef6\u7684\u8def\u5f84\u5199\u5165\u5230\u6587\u4ef6 input.fofn \u4e2d\u7528\u4e8e\u8f6f\u4ef6\u8f93\u5165\u3002<\/p>\n<p>FALCON\u8f6f\u4ef6\u8fd0\u884c\u7684\u96be\u70b9\u5728\u4e8e\u5176\u914d\u7f6e\u6587\u4ef6fc_run.cfg\u7684\u7f16\u5199\u3002\u4e00\u4e2afc_run.cfg\u793a\u4f8b\u5982\u4e0b\uff1a<\/p>\n<pre>\r\n[General]\r\n## \u8bbe\u7f6e\u4efb\u52a1\u63d0\u4ea4\u65b9\u5f0f\r\n# jobtype\u7684\u9ed8\u8ba4\u503c\u5e94\u8be5\u662fSGE\uff0c\u8868\u793a\u4f7f\u7528SGE\u96c6\u7fa4\u8fdb\u884c\u8ba1\u7b97\uff1b\r\n# local\u8868\u793a\u4f7f\u7528\u672c\u5730\u4e3b\u673a\u8fd0\u884cFALCON\uff0c\u517c\u5bb9\u6027\u6700\u597d\uff0c\u6bd5\u7adf\u96c6\u7fa4\u7684\u90e8\u7f72\u975e\u5e38\u9ebb\u70e6\uff1b\r\njob_type = local\r\n\r\n## \u6570\u636e\u8f93\u5165\r\n# \u8bbe\u7f6e\u8f93\u5165\u6587\u4ef6\u4e3ainput.fofn\uff0c\u8be5\u6587\u4ef6\u4e2d\u5305\u542b\u6709PacBio\u6570\u636e\u7684fasta\u6587\u4ef6\u3002\u6b64\u5916\u4e5f\u53ef\u4ee5\u8f93\u5165dexta\u683c\u5f0f\u7684\u6587\u4ef6\u3002dexta\u683c\u5f0f\u662fPacbio\u6d4b\u5e8f\u7ed3\u679ch5\u7684\u4e00\u79cd\u538b\u7f29\u7ed3\u679c\uff0c\u80fd\u6781\u5927\u538b\u7f29\u6d4b\u5e8f\u6570\u636e\u6587\u4ef6\u7684\u5927\u5c0f\u3002\u53ef\u4ee5\u4f7f\u7528FALCON\u8f6f\u4ef6\u9644\u5e26\u7684\u547d\u4ee4dexta\u5c06fasta\u6587\u4ef6\u8f6c\u6362\u4e3adexta\u683c\u5f0f\u3002\r\ninput_fofn = input.fofn\r\n# \u8bbe\u7f6e\u8f93\u5165\u6570\u636e\u4e3a\u539f\u59cb\u6d4b\u5e8f\u6570\u636e\uff0c\u6216\u8005\u4e3a\u4fee\u6b63\u540e\u7684\u6570\u636e\u3002\r\ninput_type = raw\r\n#input_type = preads\r\n\r\n## \u5bf9PacBio\u6570\u636e\u8fdb\u884c\u6821\u6b63\uff1a\u5bf9Pacbio raw subreads\u8fdb\u884coverlapping\u3001consensus\u548cpre-assembly\u5206\u6790\uff0c\u5bf9reads\u8fdb\u884c\u6821\u6b63\u3002\r\n# \u9009\u62e9\u957f\u5ea6\u9ad8\u4e8e\u6307\u5b9a\u9608\u503c\u7684reads\u8fdb\u884c\u5206\u6790\r\nlength_cutoff = 12000\r\n# \u9009\u62e9\u957f\u5ea6\u9ad8\u4e8e\u6307\u5b9a\u9608\u503c\u7684reads\u8fdb\u884c\u9884\u7ec4\u88c5\r\nlength_cutoff_pr = 12000\r\n# \u8c03\u7528<a href=\"https:\/\/github.com\/thegenemyers\/DAZZ_DB\" target=\"_blank\">fasta2DB<\/a>\u547d\u4ee4\u5c06reads\u6570\u636e\u5206\u5272\u6210\u591a\u4efdBlocks\u3002\r\n# -s50 \u53c2\u6570\u8868\u793a\u6bcf\u4efd\u6570\u636e\u542b\u670950Mbp\u7684\u6570\u636e\u91cf\uff0c\u8be5\u53c2\u6570\u9ed8\u8ba4\u503c\u4e3a200\uff0c\u9ed8\u8ba4\u53c2\u6570\u60c5\u51b5\u4e0b\uff0c\u4f7f\u7528daligner\u8fdb\u884c\u6bd4\u5bf9\u9700\u8981\u6d88\u8017\u7ea616G\u5185\u5b58\u3002\r\n# -x500 \u53c2\u6570\u8868\u793aread\u957f\u5ea6\u4f4e\u4e8e500bp\u7684\u4f1a\u88ab\u5ffd\u7565\u6389\u3002\r\n# -a \u53c2\u6570\u8868\u793a\u6765\u540c\u4e00\u4e2a\u81ea\u96f6\u7ea7\u6ce2\u5bfc\u5b54\u7684\u7b2c\u4e8c\u4e2aread\u4e0d\u4f1a\u88ab\u5ffd\u7565\u6389\u3002\r\npa_DBsplit_option = -x500 -s50\r\n# \u8c03\u7528<a href=\"https:\/\/github.com\/thegenemyers\/DALIGNER\" target=\"_blank\">daligner<\/a>\u5bf9\u6240\u6709Blocks\u8fdb\u884cOverlapping\u5206\u6790\u3002\r\n# -v \u53c2\u6570\u8868\u793a\u8f93\u51fadaligner\u7a0b\u5e8f\u8fd0\u884c\u4fe1\u606f\r\n# -B4 \u53c2\u6570\u8868\u793a\u6bcf\u4e2adaligner\u547d\u4ee4\u5bf94\u4e2aBlocks\u8fdb\u884cOverlapping\u5206\u6790\u3002\u8be5\u53c2\u6570\u7684\u503c\u8d8a\u5927\uff0c\u5219\u6bcf\u4e2adaligner\u547d\u4ee4\u7684\u8ba1\u7b97\u91cf\u8d8a\u5927\uff0c\u4f46\u662f\u603b\u7684\u4efb\u52a1\u6570\u8d8a\u5c11\u3002\u8be5\u53c2\u6570\u7b49\u540c\u4e8e\u4ee5\u524d\u7684-dal\r\n# -k -w -h \u53c2\u6570\u8bbe\u7f6e\u5339\u914d\u7684kmer\u76f8\u5173\u53c2\u6570\uff0c\u5176\u9ed8\u8ba4\u503c\u5206\u522b\u4e3a 14,6,35 \u3002\r\n# -T4 \u8868\u793a\u6bcf\u4e2adaligner\u4f7f\u75284\u4e2a\u7ebf\u7a0b\u8fdb\u884c\u8ba1\u7b97\uff0c\u8be5\u53c2\u6570\u9ed8\u8ba4\u503c\u662f4\uff0c\u8be5\u53c2\u6570\u53ef\u4ee5\u8bbe\u7f6e\u62102,4,8,16,32...\u3002\r\n# -M32 \u8868\u793a\u6bcf\u4e2adaligner\u547d\u4ee4\u4f7f\u752832G\u5185\u5b58\uff0c\u52a0\u5165\u8be5\u53c2\u6570\u8d77\u5230\u9650\u5236\u5185\u5b58\u4f7f\u7528\u7684\u4f5c\u7528\uff0c\u5bf9\u5927\u57fa\u56e0\u7ec4\u6bd4\u8f83\u6709\u7528\u3002\r\n# -t16 \u53c2\u6570\u8868\u793a\u8fc7\u6ee4\u6389\u8986\u76d6\u5ea6\u9ad8\u4e8e16\u7684kmer\uff0c\u8fd9\u4e9bkmer\u4f1a\u5bfc\u81f4\u5185\u5b58\u4f7f\u7528\u8fc7\u591a\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0cdaligner\u53ef\u4ee5\u6839\u636e-M\u53c2\u6570\u7684\u503c\u81ea\u52a8\u8ba1\u7b97\u672c\u53c2\u6570\u7684\u503c\u3002\r\n# -l1000 \u53c2\u6570\u8868\u793a\u5ffd\u7565\u957f\u5ea6\u4f4e\u4e8e1000bp\u7684reads\u3002\r\n# -s1000 \u53c2\u6570\u8868\u793a\u8bb0\u5f55\u6bd4\u5bf9\u7ed3\u679c\u65f6\u4ee5\u6bcf1000bp\u4e3a\u4e00\u4e2a\u8bb0\u5f55\u70b9\uff0c\u76f8\u6bd4\u4e8e\u9ed8\u8ba4\u503c100\uff0c\u80fd\u5c11\u5f88\u591a\u8bb0\u5f55\u70b9\u3002\r\n# \u4f7f\u7528daligner\u7684\u9ed8\u8ba4\u53c2\u6570\u80fd\u5f88\u597d\u5730\u5904\u7406raw pacbio\u6570\u636e\u3002\r\n# \u800c\u5bf9corrected pacbio\u6570\u636e\uff0c\u63a8\u8350\u4f7f\u7528-k20 -h60 -e.85\u53c2\u6570\u3002\r\npa_HPCdaligner_option = -v -B4 -k14 -T8 -t16 -e.70 -l1000 -s1000\r\n# FALCON\u4f7f\u7528fc_consensus.py\u8c03\u7528C\u8bed\u8a00\u5199\u7684\u7a0b\u5e8f\u6765\u6839\u636edaligner\u8fdb\u884cOverlapping\u5206\u6790\u7684\u7ed3\u679c\u8fdb\u884cconsensus\u5206\u6790\uff0c\u4ece\u800c\u5bf9subreads\u8fdb\u884c\u6821\u6b63\u3002\r\n# --min_cov \u53c2\u6570\u8bbe\u7f6e\u5f53read\u5e8f\u5217\u4e0a\u67d0\u4f4d\u70b9\u8986\u76d6\u5ea6\u4f4e\u4e8e\u6307\u5b9a\u9608\u503c\u65f6\uff0c\u5bf9read\u8fdb\u884c\u6253\u65ad\u6216\u622a\u77ed\uff0c\u9ed8\u8ba4\u503c\u662f6\u3002\r\n# --min_cov_aln \u53c2\u6570\u8bbe\u7f6e\u5f53read\u5e8f\u5217\u7684\u5e73\u5747\u8986\u76d6\u5ea6\u4f4e\u4e8e\u6307\u5b9a\u9608\u503c\u65f6\uff0c\u76f4\u63a5\u7565\u8fc7\u8be5read\uff0c\u9ed8\u8ba4\u503c\u662f10\u3002\r\n# --min_n_read \u548c --max_n_read \u53c2\u6570\u8bbe\u5b9a\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u5305\u542b\u7684reads\u6570\u5728\u6b64\u8303\u56f4\u5185\u624d\u80fd\u5f97\u5230consensus\u7ed3\u679c\uff0c\u5176\u9ed8\u8ba4\u503c\u5206\u522b\u662f10\u548c500\u3002\u5bf9\u4e8e\u57fa\u56e0\u7ec4\u91cd\u590d\u7a0b\u5ea6\u8f83\u9ad8\u7684\u60c5\u51b5\uff0c\u8981\u8bbe\u7f6e\u8f83\u4f4e\u7684--max_n_read\u503c\u6765\u51cf\u5c11\u5bf9\u91cd\u590d\u533a\u57df\u8fdb\u884cconsensus\u5206\u6790\u7684\u8ba1\u7b97\u6d88\u8017\u3002\r\n# --min_idt \u53c2\u6570\u8bbe\u7f6e\u6700\u5c0fidentity\u7684\u6bd4\u5bf9\u7ed3\u679c\u80fd\u7528\u4e8ereads\u6821\u6b63\u3002\r\n# --n_core \u53c2\u6570\u8bbe\u7f6e\u5141\u8bb8\u7684\u7ebf\u7a0b\u6570\uff0c\u9ed8\u8ba4\u503c\u662f24\u3002\r\nfalcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 8\r\n# \u8bbe\u7f6e\u8fd0\u884cdaligner\u4efb\u52a1\u7684\u5e76\u53d1\u6570\u3002\u6ce8\u610f\u7684\u662fdaligner\u548cfc_consensus.py\u4efb\u52a1\u672c\u8eab\u53ef\u4ee5\u591a\u7ebf\u7a0b\uff0c\u56e0\u6b64\u603b\u7684\u8ba1\u7b97\u9700\u6c42\u662f\u7ebf\u7a0b\u6570*\u5e76\u53d1\u6570\u3002\u82e5\u662f\u603b\u7684\u8ba1\u7b97\u9700\u8981\u8fdc\u8fdc\u8d85\u8fc7\u670d\u52a1\u5668\u7684\u8ba1\u7b97\u8d44\u6e90\uff0c\u5bb9\u6613\u5bfc\u81f4\u5b95\u673a\u3002\r\nda_concurrent_jobs = 10\r\nla_concurrent_jobs = 2\r\n# \u8bbe\u7f6e\u8fd0\u884cfc_consensus.py\u4efb\u52a1\u7684\u5e76\u53d1\u6570\u3002\u6ce8\u610f\u7684\u662fdaligner\u548cfc_consensus.py\u4efb\u52a1\u672c\u8eab\u53ef\u4ee5\u591a\u7ebf\u7a0b\uff0c\u56e0\u6b64\u603b\u7684\u8ba1\u7b97\u9700\u6c42\u662f\u7ebf\u7a0b\u6570*\u5e76\u53d1\u6570\u3002\u82e5\u662f\u603b\u7684\u8ba1\u7b97\u9700\u8981\u8fdc\u8fdc\u8d85\u8fc7\u670d\u52a1\u5668\u7684\u8ba1\u7b97\u8d44\u6e90\uff0c\u5bb9\u6613\u5bfc\u81f4\u5b95\u673a\u3002\r\ncns_concurrent_jobs = 20\r\n# \u8bbe\u7f6e\u5728SGE\u96c6\u7fa4\u8fd0\u884c\u7684\u5e76\u53d1\u6570\r\nsge_option_da = -pe smp 8 -q jobqueue\r\nsge_option_la = -pe smp 2 -q jobqueue\r\nsge_option_fc = -pe smp 80 -q jobqueue\r\nsge_option_cns = -pe smp 16 -q jobqueue\r\n\r\n## \u5bf9\u6821\u6b63\u540e\u7684reads\u8fdb\u884coverlapping\u5206\u6790\uff0c\u5176\u53c2\u6570\u548c\u4e0a\u4e00\u4e2a\u6b65\u9aa4\u7684\u53c2\u6570\u4e00\u81f4\u3002\r\novlp_DBsplit_option = -x500 -s50\r\novlp_HPCdaligner_option = -v -B4 -k20 -h60 -T8 -t32 -e.96 -l500 -s1000\r\n# \u8bbe\u7f6e\u5bf9\u6821\u6b63\u540ereads\u8fd0\u884cdaligner\u4efb\u52a1\u7684\u5e76\u53d1\u6570\u3002\r\npda_concurrent_jobs = 10\r\npla_concurrent_jobs = 2\r\nsge_option_pda = -pe smp 8 -q jobqueue\r\nsge_option_pla = -pe smp 2 -q jobqueue\r\n\r\n## \u8fc7\u6ee4overlaps\r\n# \u82e5reads\u9996\u5c3e\u4e24\u7aef\u7684\u8986\u76d6\u5ea6\u6bd4\u5e73\u5747\u8986\u76d6\u5ea6\u5927\u5f88\u591a\uff0c\u5219\u8868\u660ereads\u9996\u5c3e\u662f\u91cd\u590d\u5e8f\u5217\uff1b\u82e5reads\u9996\u5c3e\u4e24\u7aef\u7684\u8986\u76d6\u5ea6\u6bd4\u5e73\u5747\u8986\u76d6\u5ea6\u76f8\u5dee\u8f83\u5c0f\u5f88\u591a\uff0c\u5219\u8868\u660ereads\u9996\u5c3e\u51fa\u73b0\u9519\u8bef\u7684\u53ef\u80fd\u6027\u5f88\u5927\u3002\u9700\u8981\u8fc7\u6ee4\u6389\u8fd9\u79cdreads\u7684overlaps\u7ed3\u679c\u3002\u8be5\u6b65\u9aa4\u7684\u53c2\u6570\u8bbe\u7f6e\u4e0d\u5bf9\uff0c\u5bb9\u6613\u5bfc\u81f4overlaps\u5168\u90e8\u88ab\u8fc7\u6ee4\u6389\uff0c\u5f97\u4e0d\u5230\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7684\u7ed3\u679c\u3002\r\n# --bestn\u8bbe\u7f6e\u62a5\u544areads\u6b64\u6570\u76ee\u7684\u6700\u4f18overlaps\u3002\r\n# --min_cov\u548c--max_cov\u8868\u793a\u6240\u5141\u8bb8\u7684reads\u9996\u5c3e\u7684\u8986\u76d6\u5ea6\u8303\u56f4\u3002\u5bf9\u4e8e\u901a\u8fc7length_cutoff\u5f97\u5230 >20x \u6821\u6b63\u540e\u7684\u6570\u636e\u8fdb\u884c\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u53ef\u4ee5\u8bbe\u7f6e--min_cov\u503c\u4e3a5\uff0c\u8bbe\u7f6e--max_cov\u4e3a\u5e73\u5747\u8986\u76d6\u5ea6\u76843\u500d\u3002\u82e5\u7528\u4e8e\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7684\u6570\u636e\u91cf\u8f83\u5c11\uff0c\u53ef\u4ee5\u8bbe\u7f6e\u8be5\u503c\u4e3a1\u62162\u3002\r\n# --max_diff\u8bbe\u7f6e\u6240\u5141\u8bb8\u7684\u9996\u5c3e\u8986\u76d6\u5ea6\u503c\u7684\u6700\u5927\u5dee\u5f02\u3002\u8bbe\u7f6e\u8be5\u53c2\u6570\u7684\u503c\u4e3a\u5e73\u5747\u8986\u76d6\u5ea6\u76842\u500d\u3002\r\n# \u5bf9\u4e8e\u7279\u6b8a\u60c5\u51b5\uff0c\u53ef\u4ee5\u8bbe\u7f6e\u66f4\u9ad8\u7684--max_cov\u548c--max_diff\u503c\u3002\r\n# \u53ef\u4ee5\u4f7f\u7528\u57281-preads_ovl\u76ee\u5f55\u4e0b\u8fd0\u884c fc_ovlp_stats.py --fofn merge-gather\/las.fofn \u5bfc\u51faoverlap\u7ed3\u679c\u9996\u5c3e\u7684\u8986\u76d6\u5ea6\u7ed3\u679c\uff0c\u4ece\u800c\u5e2e\u52a9\u8bbe\u7f6e\u4ee5\u4e0a\u53c2\u6570\r\noverlap_filtering_setting = --max_diff 50 --max_cov 75 --min_cov 5 --bestn 10\r\n<\/pre>\n<h1>5. FALCON\u7ed3\u679c\u6587\u4ef6<\/h1>\n<pre>\r\n0-rawreads\/\r\n    \u8be5\u76ee\u5f55\u5b58\u653e\u5bf9raw subreads\u8fdb\u884coverlpping\u5206\u6790\u4e0e\u6821\u6b63\u7684\u7ed3\u679c\uff1b\r\n    \u4ee5job_\u524d\u7f00\u7684\u6587\u4ef6\u5939\u7684\u8868\u793adaligner\u4efb\u52a1\u7684\u7ed3\u679c\uff1b\r\n    \u4ee5m_\u524d\u7f00\u7684\u6587\u4ef6\u5939\u8868\u793a\u6574\u5408\u4efb\u52a1\u7684\u7ed3\u679c\uff0c\u5bf9raw subreads\u8fdb\u884coverlapping\u5206\u6790\u7684\u6bd4\u5bf9\u7ed3\u679c\u662flas\u6587\u4ef6\uff0c\u4f4d\u4e8e\u8fd9\u4e9b\u6587\u4ef6\u5939\u4e2d\uff1b\r\n    merge-gather\u4e2d\u5b58\u653e\u7740las.fofn\u6587\u4ef6\uff0c\u8be5\u6587\u4ef6\u4e2d\u5b58\u653e\u7740las\u6587\u4ef6\u7684\u8def\u5f84\u4fe1\u606f\uff1b\r\n    preads\u76ee\u5f55\u4e0b\u4fdd\u5b58\u7740\u6821\u6b63\u540e\u7684reads\u4fe1\u606f\uff0c\u4f4d\u4e8ecns_\u524d\u7f00\u76ee\u5f55\u4e0b\u7684fasta\u6587\u4ef6\u3002\r\n\r\n1-preads_ovl\/\r\n    \u8be5\u76ee\u5f55\u5b58\u653e\u5bf9\u6821\u6b63\u540ereads\u8fdb\u884coverlapping\u7684\u7ed3\u679c\uff1b\r\n    \u4ee5job_\u524d\u7f00\u7684\u6587\u4ef6\u5939\u7684\u8868\u793adaligner\u4efb\u52a1\u7684\u7ed3\u679c\uff1b\r\n    \u4ee5m_\u524d\u7f00\u7684\u6587\u4ef6\u5939\u8868\u793a\u6574\u5408\u4efb\u52a1\u7684\u7ed3\u679c\uff0c\u5bf9\u6821\u6b63\u540ereads\u8fdb\u884coverlapping\u5206\u6790\u7684\u6bd4\u5bf9\u7ed3\u679c\u662flas\u6587\u4ef6\uff0c\u4f4d\u4e8e\u8fd9\u4e9b\u6587\u4ef6\u5939\u4e2d\uff1b\r\n    merge-gather\u4e2d\u5b58\u653e\u7740las.fofn\u6587\u4ef6\uff0c\u8be5\u6587\u4ef6\u4e2d\u5b58\u653e\u7740las\u6587\u4ef6\u7684\u8def\u5f84\u4fe1\u606f\uff1b\r\n\r\n2-asm-falcon\/\r\n    \u8be5\u76ee\u5f55\u662f\u6700\u7ec8\u7ed3\u679c\u76ee\u5f55\uff0c\u5305\u542bdraft contigs\u7ed3\u679c\u6587\u4ef6p_ctg.fa\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. \u5b89\u88c5FALCON $ cd \/opt\/biosoft $ export G &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2465\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/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\/2465"}],"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=2465"}],"version-history":[{"count":14,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2465\/revisions"}],"predecessor-version":[{"id":2483,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2465\/revisions\/2483"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2465"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2465"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2465"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}