{"id":2755,"date":"2019-04-09T01:34:59","date_gmt":"2019-04-08T17:34:59","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2755"},"modified":"2019-04-09T01:41:19","modified_gmt":"2019-04-08T17:41:19","slug":"%e4%bd%bf%e7%94%a8falcon%e5%af%b9%e4%b8%89%e4%bb%a3%e6%b5%8b%e5%ba%8f%e6%95%b0%e6%8d%ae%e8%bf%9b%e8%a1%8c%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%bb%84%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2755","title":{"rendered":"\u4f7f\u7528FALCON\u5bf9\u4e09\u4ee3\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"\n<h2>1. FALCON\u8f6f\u4ef6\u7b80\u4ecb<\/h2>\n\n\n\n<p>FALCON\u662fPacBio\u516c\u53f8\u5f00\u53d1\u7684\u4e00\u6b3e\u7528\u4e8e\u4e09\u4ee3\u57fa\u56e0\u7ec4<em>De novo<\/em>\u7ec4\u88c5\u8f6f\u4ef6\u3002\u76f8\u6bd4\u4e8eHGAP4\u8f6f\u4ef6\uff0cFALCON\u8f6f\u4ef6\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u539f\u7406\u57fa\u672c\u4e00\u81f4\u3002\u4f46FALCON\u4f7f\u7528\u547d\u4ee4\u884c\u8fd0\u884c\uff0c\u66f4\u9002\u5408\u4e8e\u5927\u57fa\u56e0\u7ec4\u7684\u7ec4\u88c5\uff0c\u4e14\u80fd\u5206\u6790\u53cc\u500d\u4f53\u5e8f\u5217\uff0c\u5e76\u5728\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\u4e2d\u7ed9\u51fa\u5305\u542b\u53d8\u5f02\u4f4d\u70b9\u4fe1\u606f\u7684\u7b49\u4f4d\u57fa\u56e0\u5e8f\u5217\uff08alternative contigs \/ a-contigs\uff09\u548c\u4e3b\u8981\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\uff08primary contig \/ p-contig\uff09\u3002\u6bcf\u4e00\u6761a-contig\u90fd\u6709\u5176\u5bf9\u5e94\u7684p-contig\u5e8f\u5217\u3002\u56e0\u6b64\uff0cFALCON\u8f6f\u4ef6\u9002\u5408\u53cc\u500d\u4f53\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u80fd\u7ed9\u51fa\u5355\u500d\u7684\u57fa\u56e0\u5e8f\u5217\u3002\u5176\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\u4e2d\u7684p-contigs\u5e8f\u5217\u603b\u957f\u5ea6\u8981\u5c0f\u4e8e\u5176\u5b83\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\uff08\u4f8b\u5982Canu\u548cHGAP\uff09\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002 <\/p>\n\n\n\n<p>FALCON-Unzip\u5219\u662f\u771f\u6b63\u7684\u5355\u500d\u578b\u7ec4\u88c5\u8f6f\u4ef6\uff0c\u5b83\u80fd\u5728FALCON\u6216HGAP4\u8f6f\u4ef6\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c\u57fa\u7840\u4e0a\uff0c\u5229\u7528\u8f83\u957f\u7684PacBio reads\u8fdb\u884c\u5355\u500d\u578b\u5206\u6790\uff0c\u5bf9p-contigs\u5e8f\u5217\u5411\u5355\u500d\u578b\u8fdb\u884c\u8f6c\u6362\uff0c\u540c\u65f6\u8f93\u51fa\u5355\u500d\u578b\u5e8f\u5217\uff08haplotig\uff09\u533a\u5757\u3002 <\/p>\n\n\n\n<h2>2. FALCON\u8f6f\u4ef6\u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h2>\n\n\n\n<p>FALCON\u8f6f\u4ef6\u57282018\u5e74\u5728\u7b97\u6cd5\u4e0a\u6709\u4e86\u8f83\u5927\u7684\u66f4\u6539\uff0c\u5c06FALCON\u5728\u5185\u7684\u591a\u4e2a\u8f6f\u4ef6\u6574\u5408\u5230\u4e86pb-assembly\u8f6f\u4ef6\uff08https:\/\/github.com\/PacificBiosciences\/pb-assembly\uff09\u4e2d\u3002\u540c\u65f6\u63d0\u4f9b\u5feb\u6377\u7684bioconda\u5b89\u88c5\u65b9\u6cd5\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ wget https:\/\/repo.continuum.io\/miniconda\/Miniconda3-latest-Linux-x86_64.sh\n$ sh Miniconda3-latest-Linux-x86_64.sh\n    \u8fdb\u5165\u4ea4\u4e92\u5f0f\u754c\u9762\uff1a\u9996\u5148\uff0c\u8f93\u5165yes\uff0c\u6309Enter\u952e\uff0c\u8868\u793a\u540c\u610f\u8f6f\u4ef6\u7684license\uff1b\u7136\u540e\uff0c\u8f93\u5165conda\u7a0b\u5e8f\u5b89\u88c5\u8def\u5f84\/opt\/biosoft\/miniconda3_for_pb-assembly\uff0c\u6309enter\u952e\uff1b \u518d\u8bbe\u7f6e\u662f\u5426\u6dfb\u52a0Minicoda3\u5230PATH\u53d8\u91cf\uff0c\u76f4\u63a5\u6309Enter\u952e\uff0c\u8868\u793a\u9009\u62e9no\uff0c\u4ee5\u514d\u548c\u7cfb\u7edf\u81ea\u5e26\u7684\u8f6f\u4ef6\u51b2\u7a81\u3002\u82e5\u9700\u8981\u5207\u6362\u5230miniconda3\u73af\u5883\uff0c\u8f93\u5165\u547d\u4ee4export PATH=\/opt\/biosoft\/miniconda3_for_pb-assembly\/bin:$PATH\u5373\u53ef\u3002\n$ export PATH=\/opt\/biosoft\/miniconda3_for_pb-assembly\/bin:$PATH\n$ conda config --add channels defaults\n$ conda config --add channels bioconda\n$ conda config --add channels conda-forge\n    \u914d\u7f6ebioconda channel\uff08https:\/\/bioconda.github.io\/index.html\uff09\n$ conda install pb-assembly\n    \u5b89\u88c5pb-assembly\u8f6f\u4ef6\n$ source activate \/opt\/biosoft\/miniconda3_for_pb-assembly\n    \u6fc0\u6d3bFALCON\u8f6f\u4ef6\u7684\u8fd0\u884c\u73af\u5883<\/code><\/pre>\n\n\n\n<h2>3. FALCON\u8f6f\u4ef6\u7684\u4f7f\u7528<\/h2>\n\n\n\n<p>FALCON\u8f6f\u4ef6\u8fd0\u884c\u793a\u4f8b\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>\u9996\u5148\uff0c\u8f7d\u5165FALCON\u8f6f\u4ef6\u7684\u8fd0\u884c\u73af\u5883\u3002\n\n\u7136\u540e\uff0c\u51c6\u5907\u4e09\u79cd\u8f93\u5165\u6587\u4ef6\uff1a\u6d4b\u5e8f\u6570\u636eFASTA\u683c\u5f0f\u6587\u4ef6\u3001\u5305\u542b\u6d4b\u5e8f\u6570\u636e\u6587\u4ef6\u8def\u5f84\u7684FOFN\u5217\u8868\u6587\u4ef6\u3001\u7a0b\u5e8f\u8fd0\u884c\u7684\u53c2\u6570\u914d\u7f6e\u6587\u4ef6\u3002\u4e0b\u8f7d\u57fa\u56e0\u7ec4\u5927\u5c0f\u4e3a4.6Mb\u7684E. coli\u57fa\u56e0\u7ec4PacBio\u6d4b\u5e8f\u6570\u636e\u3002\n$ curl -L https:\/\/downloads.pacbcloud.com\/public\/data\/git-sym\/ecoli.m140913_050931_42139\\\n_c100713652400000001823152404301535_s1_p0.subreads.tar | tar xvf -\n$ ls *\/ecoli.?.fasta > input.fofn\n$ wget https:\/\/pb-falcon.readthedocs.io\/en\/latest\/_downloads\/fc_run_ecoli_local.cfg\n\u5f53\u4f7f\u7528\u6700\u65b0\u7248\u7684FALCON\u8fdb\u884c\u7ec4\u88c5\u65f6\uff0c\u9700\u8981\u5bf9\u6b64\u914d\u7f6e\u6587\u4ef6\u8fdb\u884c\u4e00\u4e9b\u4fee\u6539\u3002\n\n\u6700\u540e\uff0c\u5bf9E. coli\u57fa\u56e0\u7ec4\u8fdb\u884c\u7ec4\u88c5\n$ fc_run.py fc_run_ecoli_local.cfg\n\n\u751f\u6210\u7684\u6700\u7ec8\u4e3b\u8981\u7ed3\u679c\u6587\u4ef6\u4e3a 2-asm-falcon\/p_ctg.fa \u3002<\/code><\/pre>\n\n\n\n<p> \u8fd0\u884cFALCON\u6700\u5173\u952e\u7684\u6b65\u9aa4\u662f\u51c6\u5907\u914d\u7f6e\u6587\u4ef6fc_run.cfg\u3002\u4e00\u4e2a\u914d\u7f6e\u6587\u4ef6\u793a\u4f8b\u53ca\u5176\u53c2\u6570\u8bb2\u89e3\u5982\u4e0b\uff1a <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>[General]\n\u8f93\u5165\u53c2\u6570\uff1a\ninput_fofn = input.fofn\n\u8bbe\u7f6e\u6570\u636e\u8f93\u5165\u6587\u4ef6\u4e3ainput.fofn\uff0c\u8be5\u6587\u672c\u6587\u4ef6\u4e2d\u6bcf\u884c\u662f\u4e00\u4e2aPacBio\u6d4b\u5e8f\u6570\u636e\u7684FASTA\u6587\u4ef6\u8def\u5f84\u3002\u53ef\u4ee5\u4f7f\u7528\u76f8\u5bf9\u8def\u5f84\u3002\ninput_type = raw\n\u8bbe\u7f6e\u8f93\u5165\u6570\u636e\u7c7b\u578b\u4e3a\u539f\u59cb\u6d4b\u5e8f\u6570\u636e\uff08raw\uff09\uff0c\u6216\u8005\u4e3a\u4fee\u6b63\u540e\u7684\u6570\u636e\uff08preads\uff09\u3002\n\n\u5bf9\u6570\u636e\u8fdb\u884c\u5206\u5757\uff1a\npa_DBsplit_option = -x500 \u2013s200\n\u8bbe\u7f6e\u9884\u7ec4\u88c5\uff08pre-assembly\uff09\u8fc7\u7a0b\u4e2d\u5bf9raw reads\u6570\u636e\u8fdb\u884c\u5206\u5757\u7684\u53c2\u6570\u3002\u8fd9\u4e9b\u53c2\u6570\u4f1a\u4f20\u9012\u7ed9Dbsplit\u547d\u4ee4\u6765\u6267\u884c\u6570\u636e\u5206\u5757\u3002\n-s&lt;int>    default: 200\n\u8868\u793a\u6bcf\u4efd\u6570\u636e\u542b\u670950Mb\u7684\u6570\u636e\u91cf\uff0c\u8be5\u53c2\u6570\u9ed8\u8ba4\u503c\u4e3a200\u3002\u9ed8\u8ba4\u53c2\u6570\u60c5\u51b5\u4e0b\uff0c\u4f7f\u7528daligner\u8fdb\u884c\u6bd4\u5bf9\u9700\u8981\u6d88\u8017\u7ea616G\u5185\u5b58\u3002\u63a8\u8350\u8bbe\u7f6e\u8be5\u53c2\u6570\u7684\u503c\u4e3a\u9884\u6d4b\u7684\u57fa\u56e0\u7ec4\u5927\u5c0f\u3002\u6b64\u5916\uff0c\u8f6f\u4ef6\u4f5c\u8005\u63a8\u8350\u5bf9\u5c0f\u4e8e10Mb\u7684\u57fa\u56e0\u7ec4\u8bbe\u7f6e\u8be5\u53c2\u6570\u503c\u4e3a50\uff0c\u5bf9\u4e8e\u5927\u57fa\u56e0\u7ec4\u8bbe\u7f6e\u8be5\u53c2\u6570\u503c\u4e3a200\u3002\n-x&lt;int>\n\u5ffd\u7565\u957f\u5ea6\u5c0f\u4e8e\u6307\u5b9a\u9608\u503c\u7684reads\u3002\novlp_DBsplit_option=-x500 \u2013s200\n\u8bbe\u7f6eOLC\u7ec4\u88c5\u8fc7\u7a0b\u4e2d\u5bf9preads\u6570\u636e\u8fdb\u884c\u5206\u5757\u7684\u53c2\u6570\u3002\n\n\u5bf9\u91cd\u590d\u5e8f\u5217\u8fdb\u884c\u5c4f\u853d\uff1a\npa_HPCTANmask_option = -k18 -h480 -w8 -e.80\n\u8bbe\u7f6e\u5728\u9884\u7ec4\u88c5\u8fc7\u7a0b\u5bf9\u4e32\u8054\u91cd\u590d\u8fdb\u884c\u5c4f\u853d\u7684\u53c2\u6570\u3002\u5176\u53c2\u6570\u4f1a\u4f20\u9012\u7ed9HPC.TANmask\u547d\u4ee4\u3002\u8be5\u547d\u4ee4\u662f\u6b63\u5e38daligner\u547d\u4ee4\u7684\u4e00\u4e2a\u53d8\u79cd\uff0c\u9002\u5408\u5bf9\u4e32\u8054\u91cd\u590d\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\u3002\npa_HPCREPmask_option = -k18 -h480 -w8 -e.80\n\u8bbe\u7f6e\u5728\u9884\u7ec4\u88c5\u8fc7\u7a0b\u5bf9\u6563\u5728\u91cd\u590d\u8fdb\u884c\u5c4f\u853d\u7684\u53c2\u6570\u3002\u5176\u53c2\u6570\u4f1a\u4f20\u9012\u7ed9HPC.REPmask\u547d\u4ee4\u3002\u8be5\u5206\u6790\u6b65\u9aa4\u4f1a\u8fed\u4ee33\u6b21\u3002HPC.TANmask\u547d\u4ee4\u8fdb\u884c\u6570\u636e\u5206\u6790\u65f6\u6709\u4e24\u4e2a\u5173\u952e\u53c2\u6570-g\u548c-c\uff0c\u7528\u4e8e\u8bbe\u7f6e\u5206\u6790\u7684\u6570\u636e\u5757\u6570\u91cf\u548c\u8986\u76d6\u5ea6\u9608\u503c\u3002pa_REPmask_code\u8bbe\u7f6e3\u6b21\u8fed\u4ee3\u8fc7\u7a0b\u4e2d\u8fd9\u4e24\u4e2a\u53c2\u6570\u7684\u503c\u3002\u8fd9\u4e24\u4e2a\u53c2\u6570\u503c\u7684\u8bbe\u7f6e\u4e0e\u6570\u636e\u5206\u5757\u65b9\u6cd5\u548c\u6d4b\u5e8f\u6570\u636e\u91cf\u6709\u5173\u3002\npa_REPmask_code = 1,666;4,266;8,53\n\u8bbe\u7f6e\u4e09\u6b21HPC.REPmask\u547d\u4ee4\u4e2d\u7684-g\u548c-c\u53c2\u6570\u7684\u503c\u3002\u4ee5\u4e0a\u53c2\u6570\u503c\u5219\u8868\u793a\u4e0d\u5bf9\u6563\u5728\u91cd\u590d\u8fdb\u884c\u5c4f\u853d\u3002\u8be5\u53c2\u6570\u7684\u8bbe\u7f6e\u53ef\u4ee5\u53c2\u8003\u7f51\u5740https:\/\/dazzlerblog.wordpress.com\/2016\/04\/01\/detecting-and-soft-masking-repeats\/\u3002\u5728\u8be5\u6587\u7ae0\u4e2d\uff0c\u4f5c\u8005\u7ed9\u51fa\u4e86\u4e00\u4e2a\u793a\u4f8b\uff1a\u5bf930Gb\u7684\u57fa\u56e0\u7ec4\u6d4b\u5e8f30x\u5e76\u5c06\u6570\u636e\u5206\u5272\u62103600\u4e2a\u5927\u5c0f\u4e3a250Mb\u7684\u6570\u636e\u5757\uff0c\u4f7f\u7528\u53c2\u6570\u503c\u201c1,20;10,15;100,10\u201d\u3002\u6bcf\u4e2a\u6570\u636e\u5757\u7684\u6d4b\u5e8f\u6df1\u5ea6\u4e3a0.008x\uff0c\u5bf91\u4e2a\u6570\u636e\u5757\u7684\u6570\u636e\u8fdb\u884c\u6bd4\u5bf9\u540e\uff0c\u5bf9reads\u4e2d\u8986\u76d6\u5ea6\u8d85\u8fc720x\u7684\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\uff0c\u5373\u5bf9\u9ad8\u5ea6\u91cd\u590d\uff0820 \/ 0.008 = 2500x\uff09\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\uff1b\u7136\u540e\u7b2c\u4e8c\u6b21\u8fed\u4ee3\u4e2d\uff0c\u5bf910\u4e2a\u6570\u636e\u5757\u7684\u6570\u636e\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5bf9reads\u4e2d\u8986\u76d6\u5ea6\u8d85\u8fc715x\u7684\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\uff0c\u5373\u5bf9\u4e2d\u5ea6\u91cd\u590d\uff0815 \/ 0.08 = 187.5x\uff09\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\uff1b\u6700\u540e\u7b2c\u4e09\u6b21\u8fed\u4ee3\u4e2d\uff0c\u5bf9100\u4e2a\u6570\u636e\u5757\u7684\u6570\u636e\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5bf9reads\u4e2d\u8986\u76d6\u5ea6\u8d85\u8fc710x\u7684\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\uff0c\u5373\u5bf9\u4f4e\u5ea6\u91cd\u590d\uff0810 \/ 0.8 = 12.5x\uff09\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\u3002\u793a\u4f8b\u4e2d\u57fa\u56e0\u7ec4\u5927\u5c0f\u662f30Gb\uff0c\u8d85\u7ea7\u5927\uff0c\u4e00\u822c\u542b\u6709\u5927\u91cf\u91cd\u590d\u5e8f\u5217\uff0c\u4f7f\u7528\u4e0a\u8ff0\u53c2\u6570\u5bf9\u6570\u636e\u4e2d\u7684\u91cd\u590d\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\u3002\n\u5bf9\u4e8e\u5e38\u89c4\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u8bbe\u7f6epa_REPmask_code\u53c2\u6570\u540e\uff0c\u5728\u4e09\u6b21\u8fed\u4ee3\u8fc7\u7a0b\u4e2d\uff0c\u63a8\u8350\u9010\u6b65\u5bf9\u91cd\u590d\u6b21\u6570\u4e3a1000x\u3001100x\u548c10x\u7684\u5e8f\u5217\u4f4d\u70b9\u8fdb\u884c\u5c4f\u853d\u3002\u4f8b\u5982\uff1a\u5bf9300Mb\u5927\u5c0f\u7684\u57fa\u56e0\u7ec4\u6d4b\u5e8f100x\uff0c\u5c06\u6570\u636e\u5206\u5272\u6210150\u4e2a\u5927\u5c0f\u4e3a200Mb\u7684\u6570\u636e\u5757\uff0c\u53ef\u4ee5\u8003\u8651\u8bbe\u7f6epa_REPmask_code\u503c\u4e3a\u201c1,666;4,266;8,53\u201d\u3002\novlp_HPCTANmask_option = -k20 -h480 -w8 -e.80\n\u8bbe\u7f6e\u5728OLC\u7ec4\u88c5\u8fc7\u7a0b\u5bf9\u4e32\u8054\u91cd\u590d\u8fdb\u884c\u5c4f\u853d\u7684\u53c2\u6570\u3002\u5176\u53c2\u6570\u4f1a\u4f20\u9012\u7ed9HPC.TANmask\u547d\u4ee4\u3002\n\n\u9884\u7ec4\u88c5\uff08pre-assembly\uff09\u53c2\u6570\uff1a\nlength_cutoff = -1\n\u8bbe\u7f6e\u5bf9\u79cd\u5b50\u5e8f\u5217\u7684\u957f\u5ea6\u7b5b\u9009\u9608\u503c\u3002\u82e5\u8be5\u53c2\u6570\u503c\u8bbe\u7f6e\u4e3a-1\uff0c\u5219\u7a0b\u5e8f\u81ea\u52a8\u8ba1\u7b97\u79cd\u5b50\u5e8f\u5217\u7684\u957f\u5ea6\u7b5b\u9009\u9608\u503c\uff0c\u6839\u636e\u5982\u4e0b\u4e24\u4e2a\u53c2\u6570\u6311\u9009\u6700\u957f\u7684reads\u5e8f\u5217\u4f5c\u4e3a\u79cd\u5b50\u5e8f\u5217\uff0c\u76f4\u5230\u5176\u6570\u636e\u91cf\u8fbe\u5230\u57fa\u56e0\u7ec4\u6307\u5b9a\u8986\u76d6\u5ea6\u4e3a\u6b62\u3002\ngenome_size = 4652500\nseed_coverage = 30\n\u8bbe\u7f6e\u57fa\u56e0\u7ec4\u5927\u5c0f\u548c\u79cd\u5b50\u5e8f\u5217\u8986\u76d6\u5ea6\u3002\u63a8\u8350\u8bbe\u7f6eseed_coverage\u53c2\u6570\u7684\u503c\u4e3a20~40x\u3002\u5f53\u7136\u662f\u7528\u66f4\u591a\u7684\u79cd\u5b50\u5e8f\u5217\u6709\u5229\u4e8e\u57fa\u56e0\u7ec4\u7684\u7ec4\u88c5\u6548\u679c\uff0c\u4f46\u662f\u4f1a\u6d88\u8017\u66f4\u591a\u8fd0\u884c\u65f6\u95f4\u3002\npa_daligner_option = -k14 -w6 -h35 -e.70 -l1000\n\u5728\u65b0\u7248\u672cFALCON\u4e2d\u8be5\u53c2\u6570\u989d\u5916\u518d\u5206\u51fa\u4e86pa_HPCdaligner_option\u53c2\u6570\uff0c\u4e13\u95e8\u7528\u4e8e\u5bf9\u6570\u636e\u5757\u7684\u5206\u914d\u3002pa_daligner_option\u53c2\u6570\u4e13\u95e8\u7528\u4e8e\u8c03\u7528daligner\u8f6f\u4ef6\u5bf9raw reads\u8fdb\u884c\u6bd4\u5bf9\uff0c\u8fdb\u884coverlap\u5206\u6790\u3002\u5176\u5e38\u7528\u53c2\u6570\uff1a\n-k&lt;int>    default: 14\n\u8bbe\u7f6ek-mer\u5927\u5c0f\u3002\u63a8\u8350\u8bbe\u7f6e\u4e3a14~18\u3002\u8bbe\u7f6e\u8f83\u4f4e\u7684\u503c\uff0c\u80fd\u63d0\u9ad8sensitivity\uff0c\u5f97\u5230\u66f4\u591a\u7684reads\u91cd\u53e0\u7ed3\u679c\uff0c\u4f46\u589e\u52a0\u78c1\u76d8\u3001\u5185\u5b58\u3001\u8ba1\u7b97\u548c\u65f6\u95f4\u6d88\u8017\uff0c\u9002\u5408\u6570\u636e\u8d28\u91cf\u8f83\u5dee\u7684\u60c5\u51b5\uff1b\u8bbe\u7f6e\u8f83\u9ad8\u7684\u503c\uff0c\u80fd\u63d0\u9ad8specificity\uff0c\u7cfb\u7edf\u8d44\u6e90\u6d88\u8017\u66f4\u5c11\uff0c\u8fd0\u884c\u901f\u5ea6\u66f4\u5feb\uff0c\u4ec5\u9002\u5408\u6570\u636e\u8d28\u91cf\u8f83\u9ad8\u7684\u60c5\u51b5\u3002\n-w&lt;int>    default: 6\ndaligner\u547d\u4ee4\u5bf9\u4e24\u4e2areads\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5f97\u5230\u4e00\u4e2a\u659c\u5bf9\u89d2\u7ebf\u7684\u6bd4\u5bf9\u5e26\u3002\u8be5\u5e26\u7684\u5bbd\u5ea6\u8bbe\u7f6e\u4e3a2\u7684w\u6b21\u65b9\u3002\n-h&lt;int>    default: 35\n\u5728\u659c\u5bf9\u89d2\u7ebf\u5e26\u7684\u6bd4\u5bf9\u533a\u57df\u4e0a\uff0c\u9700\u8981\u81f3\u5c11\u6709\u6307\u5b9a\u6570\u76ee\u7684\u78b1\u57fa\u80fd\u88abk-mers\u8986\u76d6\u3002-k\u3001-w\u548c-h\u662fdaligner\u547d\u4ee4\u8fdb\u884c\u6bd4\u5bf9\u7684\u4e3b\u8981\u53c2\u6570\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0c\u5bfb\u627e\u4e24\u4e24reads\u4e4b\u95f4\u91cd\u53e0\uff0c\u5148\u5c06reads\u5206\u5272\u6210\u957f\u5ea6\u4e3a14bp\u7684k-mers\u5e8f\u5217\uff1b\u5bf9\u5176\u4e2d\u4e00\u6761\u5e8f\u5217\u5bbd\u5ea6\u4e3a64bp\u7684\u533a\u57df\u8fdb\u884c\u5206\u6790\uff0c\u8981\u6c42\u81f3\u5c11\u670935\u4e2a\u78b1\u57fa\u4f4d\u70b9\u80fd\u548c\u88ab\u53e6\u5916\u4e00\u6761\u5e8f\u5217\u7684k-mers\u8986\u76d6\uff0c\u5219\u627e\u5230\u91cd\u53e0\u3002\n-k\u3001-w\u548c-h\u7684\u9ed8\u8ba4\u53c2\u6570\u9002\u5408\u4e8ePacBio\u6d4b\u5e8f\u7684raw reads\u3002\u5bf9\u4e8e\u4fee\u6b63\u540e\u7684read\uff0c\u63a8\u8350\u4f7f\u7528\u53c2\u6570\u201cdaligner -k20 -h60 -e.95\u201d\u3002\n-e&lt;float>    default: 0.70\n\u8bbe\u7f6eidentity\u9608\u503c\u3002\u63a8\u8350\u8bbe\u7f6e\u4e3a0.70~0.80\u3002\u8bbe\u7f6e\u4e3a\u8f83\u9ad8\u7684\u503c\u6709\u5229\u4e8e\u5355\u500d\u578b\u5e8f\u5217\u7684\u7ec4\u88c5\u3002\n-l&lt;int>    default: 1000\n\u5ffd\u7565\u957f\u5ea6\u5c0f\u4e8e\u4f4e\u4e8e\u8bbe\u5b9a\u503c\u7684reads\u3002\n-T&lt;int>    default: 4\n\u8bbe\u7f6e\u6bcf\u4e2adaligner\u4f7f\u7528\u7684CPU\u7ebf\u7a0b\u6570\u3002\n-M&lt;int>\n\u5c1d\u8bd5\u4ec5\u4f7f\u7528\u6307\u5b9a\u5927\u5c0fGB\u7684\u5185\u5b58\u3002\u7a0b\u5e8f\u901a\u8fc7\u5ffd\u7565\u8986\u76d6\u5ea6\u8fc7\u9ad8\u7684k-mers\u6765\u964d\u4f4e\u5185\u5b58\u4f7f\u7528\u3002\u4e00\u822c\u60c5\u51b5\u4e0b\uff0c\u5bf9\npa_HPCdaligner_option = -v -B4 -M16\n\u7a0b\u5e8f\u8c03\u7528HPC.daligner\u8fdb\u884c\u5206\u6790\uff0c\u76f8\u6bd4\u4e8edaligner\u547d\u4ee4\uff0c\u5176\u589e\u52a0\u7684\u5e38\u7528\u53c2\u6570\uff1a\n-v\n\u5c06-v\u53c2\u6570\u4f20\u9012\u7ed9LAsort\u548cLAmerge\u547d\u4ee4\u3002\n-B&lt;int>    default: 4\n\u8bbe\u7f6e\u6bcf\u4e2adaligner\u4efb\u52a1\u5bf9\u6307\u5b9a\u6570\u76ee\u7684\u6570\u636e\u5757\u8fdb\u884c\u5206\u6790\u3002\u5728\u6700\u65b0\u7248\u672c\u7684FALCON\u4e2d\uff0c\u8be5\u53c2\u6570\u4e0d\u80fd\u518d\u8bbe\u7f6e\u5230pa_daligner_option\u53c2\u6570\u4e2d\uff0c\u5426\u5219\u7a0b\u5e8f\u8fd0\u884c\u51fa\u9519\u3002\nfalcon_sense_option = --output-multi --min-idt 0.70 --min-cov 4 --max-n-read 200\nFALCON\u4f7f\u7528fc_consensus\u547d\u4ee4\u6839\u636edaligner\u8fdb\u884cOverlapping\u5206\u6790\u7684\u7ed3\u679c\u8fdb\u884c\u4e00\u81f4\u6027\u5206\u6790\uff0c\u4ece\u800c\u5bf9\u79cd\u5b50\u5e8f\u5217\u8fdb\u884c\u6821\u6b63\u3002\u5e38\u7528\u53c2\u6570\uff1a\n--output-multi\n\u8f93\u51fa\u6bcf\u4e2a\u79cd\u5b50\u5e8f\u5217\u591a\u4e2a\u4fee\u6b63\u540e\u7684\u533a\u57df\u3002\n--min-cov    default: 6\n\u8bbe\u7f6e\u5f53\u79cd\u5b50\u5e8f\u5217\u4e0a\u67d0\u4f4d\u70b9\u8986\u76d6\u5ea6\u4f4e\u4e8e\u6307\u5b9a\u9608\u503c\u65f6\uff0c\u5219\u5728\u8be5\u4f4d\u70b9\u5bf9\u5e8f\u5217\u6253\u65ad\u6216\u622a\u77ed\u3002\n--min-cov-aln    default: 10\n\u8bbe\u7f6e\u5f53\u79cd\u5b50\u5e8f\u5217\u7684\u5e73\u5747\u8986\u76d6\u5ea6\u4f4e\u4e8e\u6307\u5b9a\u9608\u503c\u65f6\uff0c\u8fc7\u6ee4\u6389\u8be5\u5e8f\u5217\u3002\n--min-n-read    default: 10\n--max-n-read    default: 500\n\u5bf9\u8986\u76d6\u5ea6\u5728--min_n_read\u548c--max_n_read\u4e24\u4e2a\u53c2\u6570\u8bbe\u5b9a\u8303\u56f4\u5185\u7684\u4f4d\u70b9\u8fdb\u884c\u4e00\u81f4\u6027\u5206\u6790\uff0c\u4ece\u800c\u5bf9\u79cd\u5b50\u5e8f\u5217\u8fdb\u884c\u6821\u6b63\u3002\n--min-idt    default: 0.7\n\u8bbe\u7f6e\u6bd4\u5bf9\u7ed3\u679c\u4e2dreads\u91cd\u53e0\u90e8\u5206\u7684\u6700\u5c0fidentity\u9608\u503c\u3002\n--n-core    default: 24\n\u8bbe\u7f6e\u8fd0\u884c\u7684\u7ebf\u7a0b\u6570\uff0c\u9ed8\u8ba4\u503c\u662f24\u3002\nfalcon_sense_greedy = False\nfalcon_sense_skip_contained = False\n\nOLC\u7b97\u6cd5\u8fdb\u884c\u7ec4\u88c5\u7684\u53c2\u6570\uff1a\nlength_cutoff_pr = 12000\n\u5bf9\u9884\u7ec4\u88c5\u7ed3\u679c\u4e2d\u957f\u5ea6\u8d85\u8fc7\u6b64\u9608\u503c\u7684reads\u4f7f\u7528OLC\u7b97\u6cd5\u8fdb\u884c\u4e0b\u4e00\u6b65\u7ec4\u88c5\u3002\novlp_HPCdaligner_option = -v -B4 -M16\novlp_daligner_option = -k20 -w6 -h60 -e.96 -l1000\n\u8c03\u7528daligner\u5bf9\u6821\u6b63\u540e\u7684preads\u8fdb\u884coverlapping\u5206\u6790\u65f6\uff0c\u53c2\u6570\u76f8\u5bf9\u8981\u8bbe\u7f6e\u66f4\u52a0\u4e25\u683c\u3002\n-k&lt;int>    default: 14\n\u5bf9preads\u8fdb\u884c\u6bd4\u5bf9\uff0c\u63a8\u8350\u8be5\u53c2\u6570\u7684\u503c\u4e3a18~24\u3002\n-e&lt;float>    default: 0.70\n\u5bf9preads\u8fdb\u884c\u6bd4\u5bf9\uff0c\u63a8\u8350\u8be5\u53c2\u6570\u7684\u503c\u4e3a0.93~0.96\u3002\noverlap_filtering_setting = --max-diff 100 --max-cov 100 --min-cov 2 --bestn 10\n\u8fc7\u6ee4overlaps\u3002\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\n--bestn    default: 10\n\u8bbe\u7f6e\u62a5\u544areads\u6b64\u6570\u76ee\u7684\u6700\u4f18overlaps\u3002\n--min-cov\u548c\u2014max-cov\n\u6240\u5141\u8bb8\u7684reads\u9996\u5c3e\u7684\u8986\u76d6\u5ea6\u8303\u56f4\u3002\n--max-diff\n\u8bbe\u7f6e\u6240\u5141\u8bb8\u7684\u9996\u5c3e\u8986\u76d6\u5ea6\u503c\u7684\u6700\u5927\u5dee\u5f02\u3002\nfc_ovlp_to_graph_option = --min_len 4000 --min_idt 0.96\n\n\u4efb\u52a1\u6295\u9012\u4e0e\u8ba1\u7b97\u8d44\u6e90\u6d88\u8017\u53c2\u6570\uff1a\n[job.defaults]\njob_type = local\n\u8bbe\u7f6e\u4efb\u52a1\u63d0\u4ea4\u65b9\u5f0f\u3002local\u8868\u793a\u4f7f\u7528\u672c\u5730\u4e3b\u673a\u8fd0\u884cFALCON\uff0c\u8fd0\u884c\u76f8\u5bf9\u7a33\u5b9a\u3002\u4e5f\u53ef\u4ee5\u8bbe\u7f6e\u4e3a\u96c6\u7fa4\u4efb\u52a1\u63d0\u4ea4\u65b9\u5f0f\uff0c\u53ef\u4ee5\u8bbe\u7f6e\u7684\u503c\u6709\uff1asge\u3001lsf\u3001pbs\u3001torque\u548cslurm\u3002\u8be5\u53c2\u6570\u8bbe\u7f6e\u4e0d\u540c\u7684\u503c\uff0c\u540e\u9762\u7684submit\u4e5f\u8981\u8bbe\u7f6e\u5bf9\u5e94\u7684\u4fe1\u606f\u3002\npwatcher_type=blocking\nsubmit = bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}\nMB=32768\nNPROC=6\nnjobs=32\nFALCON\u8f6f\u4ef6\u6d41\u7a0b\u5bf9\u6570\u636e\u8fdb\u884c\u4e86\u5207\u5272\uff0c\u518d\u8fdb\u884c\u5e76\u884c\u5316\u8fd0\u7b97\uff0c\u52a0\u5feb\u7a0b\u5e8f\u8fd0\u884c\u901f\u5ea6\u3002MB\u8bbe\u7f6e\u4efb\u52a1\u5b9e\u7528\u7684\u5185\u5b58\u6570\uff1bNPROC\u8bbe\u7f6e\u5355\u4e2a\u4efb\u52a1\u7684CPU\u7ebf\u7a0b\u6570\uff1bnjobs\u8bbe\u7f6e\u5e76\u884c\u4efb\u52a1\u6570\u3002\u540e\u7eed\u5206\u522b\u5bf9\u6bcf\u4e2a\u6d41\u7a0b\u4e2d\u7684\u8ba1\u7b97\u8d44\u6e90\u8fdb\u884c\u5206\u914d\u3002da\u8868\u793a\u9884\u7ec4\u88c5\u8fc7\u7a0b\u4e2d\u8fd0\u884c\u7684daligner\u547d\u4ee4\uff1bla\u8868\u793a\u9884\u7ec4\u88c5\u8fc7\u7a0b\u4e2d\u8fd0\u884c\u7684Lasort\u548cLAmerge\u547d\u4ee4\uff1bcns\u8868\u793a\u9884\u7ec4\u88c5\u8fc7\u7a0b\u4e2d\u8fd0\u884c\u7684fc_consensus\u547d\u4ee4\uff1bpda\u8868\u793a\u8fd0\u884cOLC\u7ec4\u88c5\u8fc7\u7a0b\u4e2d\u8fd0\u884c\u7684\u7684daligner\u547d\u4ee4\uff1bpla\u8868\u793aOLC\u7ec4\u88c5\u8fc7\u7a0b\u4e2d\u8fd0\u884c\u7684Lasort\u548cLAmerge\u547d\u4ee4\uff1basm\u8868\u793a\u6700\u7ec8\u7ec4\u88c5\u8fc7\u7a0b\u3002\n[job.step.da]\nNPROC=4\nMB=32768\nnjobs=240\n[job.step.la]\nNPROC=4\nMB=32768\nnjobs=240\n[job.step.cns]\nNPROC=8\nMB=65536\nnjobs=240\n[job.step.pda]\nNPROC=4\nMB=32768\nnjobs=240\n[job.step.pla]\nNPROC=4\nMB=32768\nnjobs=240\n[job.step.asm]\nNPROC=24\nMB=196608\nnjobs=1<\/code><\/pre>\n\n\n\n<p>FALCON\u7684\u7ed3\u679c\u6587\u4ef6\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>0-rawreads\/\n\u8be5\u76ee\u5f55\u5b58\u653e\u5bf9raw subreads\u8fdb\u884coverlpping\u5206\u6790\u4e0e\u6821\u6b63\u7684\u7ed3\u679c\uff1b\n0-rawreads\/cns-runs\/cns_*\/*\/*.fasta\u5b58\u653e\u6821\u6b63\u540e\u7684\u5e8f\u5217\u4fe1\u606f\u3002\n\n1-preads_ovl\/\n\u8be5\u76ee\u5f55\u5b58\u653e\u5bf9\u6821\u6b63\u540ereads\u8fdb\u884coverlapping\u7684\u7ed3\u679c\uff1b\n\n2-asm-falcon\/\n\u8be5\u76ee\u5f55\u662f\u6700\u7ec8\u7ed3\u679c\u76ee\u5f55\uff0c\u4e3b\u8981\u7684\u7ed3\u679c\u6587\u4ef6\u662fp_ctg.fa\u548ca_ctg.fa\u3002<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. FALCON\u8f6f\u4ef6\u7b80\u4ecb FALCON\u662fPacBio\u516c\u53f8\u5f00\u53d1\u7684\u4e00\u6b3e\u7528\u4e8e\u4e09\u4ee3\u57fa\u56e0 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2755\">\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\/2755"}],"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=2755"}],"version-history":[{"count":4,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2755\/revisions"}],"predecessor-version":[{"id":3494,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2755\/revisions\/3494"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2755"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2755"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2755"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}