{"id":2436,"date":"2017-04-03T22:16:17","date_gmt":"2017-04-03T14:16:17","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2436"},"modified":"2017-04-22T15:20:11","modified_gmt":"2017-04-22T07:20:11","slug":"%e4%bd%bf%e7%94%a8dbg2olc%e5%af%b9%e4%ba%8c%e3%80%81%e4%b8%89%e4%bb%a3%e6%b7%b7%e5%90%88%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=2436","title":{"rendered":"\u4f7f\u7528DBG2OLC\u5bf9\u4e8c\u3001\u4e09\u4ee3\u6df7\u5408\u6570\u636e\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"

1. DBG2OLC\u8f6f\u4ef6\u7b80\u4ecb<\/h1>\n

DBG2OLC\u80fd\u5229\u7528\u4e8c\u4ee3\u548c\u4e09\u4ee3\u6df7\u5408\u6570\u636e\u7ec4\u88c5\u5927\u57fa\u56e0\u7ec4\u3002\u5176\u6587\u7ae0\u4e8e2016\u5e74\u53d1\u8868\u5728Scientific Reports\u4e0a\u3002<\/p>\n

2. DBG2OLC\u8f6f\u4ef6\u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h1>\n

\u4f7f\u7528git\u4e0b\u8f7dDBG2OLC\u8f6f\u4ef6<\/p>\n

\r\n$ cd \/opt\/biosoft\/\r\n$ git clone https:\/\/github.com\/yechengxi\/DBG2OLC.git\r\n$ cd \/opt\/biosoft\/DBG2OLC\r\n\u6309\u7167\u8bf4\u660e\u4e2d\u5bf9\u8f6f\u4ef6\u8fdb\u884c\u7f16\u8bd1\uff0c\u7f16\u8bd1\u51fa\u76843\u4e2a\u53ef\u6267\u884c\u7a0b\u5e8f\u5168\u90e8\u90fd\u662fDBG2OLC\u547d\u4ee4\r\n$ g++ -O3 -o SparseAssebmler DBG2OLC.cpp\r\n$ g++ -O3 -o DBG2OLC *.cpp\r\n$ g++ -O3 -o Sparc *.cpp\r\n\u76f4\u63a5\u62f7\u8d1d\u4f5c\u8005\u7f16\u8bd1\u597d\u7684\u7a0b\u5e8f\u5373\u53ef\r\n$ chmod 755 compiled\/*\r\n$ cp compiled\/* .\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/DBG2OLC' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n
DBG2OLC\u7a0b\u5e8f\u7b2c\u4e09\u6b65\u9700\u8981blasr, sparc\/pbdagcon\u8f6f\u4ef6\u652f\u6301\u3002\u5176\u4e2dsparc\u5728DBG2OLC\u5b89\u88c5\u6587\u4ef6\u5939\u4e0b\u3002
\n\u5b89\u88c5blasr<\/p>\n
\r\n\u4e0b\u8f7dBLASR\r\n$ git clone https:\/\/github.com\/PacificBiosciences\/blasr.git \/opt\/biosoft\/blasr\r\n$ cd \/opt\/biosoft\/blasr\/\r\n\u4e0b\u8f7dlibcpp\u548cpbbam\u4e24\u4e2asubmodules\r\n$ make update-submodule\r\n\r\nblasr\u7f16\u8bd1\u9700\u8981hdf5\u652f\u6301,\u4ecehdf5\u5b98\u7f51\u4e0b\u8f7d\u9002\u5408centos6\u7684\u4e8c\u8fdb\u5236\u5305\u5e76\u5b89\u88c5 \r\n$ wget https:\/\/support.hdfgroup.org\/ftp\/HDF5\/releases\/hdf5-1.10\/hdf5-1.10.0-patch1\/bin\/linux-centos6-x86_64-gcc447\/hdf5-1.10.0-patch1-linux-centos6-x86_64-gcc447-shared.tar.gz\r\n$ tar zxf hdf5-1.10.0-patch1-linux-centos6-x86_64-gcc447-shared.tar.gz -C \/opt\/sysoft\/\r\n\r\n\u53ef\u4ee5\u4f7f\u7528cmake, pitchfork\u548cmake\u4e09\u79cd\u65b9\u5f0f\u5bf9BLASR\u8fdb\u884c\u7f16\u8bd1\uff0c\u4ee5\u4e0b\u4f7f\u7528\u5e38\u89c4\u7684make\u65b9\u6cd5\u8fdb\u884c\u7f16\u8bd1\uff0c\u9700\u8981\u9ad8\u7248\u672cgcc\u652f\u6301\r\n\u5bf9BLASR\u8fdb\u884cconfigure\r\n$ .\/configure.py --shared --sub --no-pbbam HDF5_INCLUDE=\/opt\/sysoft\/hdf5-1.10.0-patch1-linux-centos6-x86_64-gcc447-shared\/include\/ HDF5_LIB=\/opt\/sysoft\/hdf5-1.10.0-patch1-linux-centos6-x86_64-gcc447-shared\/lib\/\r\n\u5bf9submodules\u8fdb\u884cconfigure\r\n$ make configure-submodule\r\n\u5bf9submodules\u8fdb\u884cmake\r\n$ make build-submodule -j 4\r\n\u5bf9BLASR\u8fdb\u884cmake\r\n$ make blasr -j 4\r\n\u5bf9\u5176\u5b83\u5de5\u5177\uff0c\u4f8b\u5982pls2fasta, loadPulses, sawriter\u7b49\u8fdb\u884c\u7f16\u8bd1\uff0c\u5176\u7ed3\u679c\u6587\u4ef6\u5728utils\u6587\u4ef6\u5939\u4e2d\r\n$ make -j 4\r\n\r\n\u53ef\u9009\u6b65\u9aa4\uff1a\u624b\u52a8\u5c06\u6709\u7528\u7684\u547d\u4ee4\u548c\u5e93\u6587\u4ef6\u653e\u7f6e\u5230\u6307\u5b9a\u7684\u5730\u65b9\r\nblasr\u7684\u6b63\u5e38\u8fd0\u884c\u9700\u8981\u4f9d\u8d56libcpp\u91cc\u9762\u4e09\u4e2a\u5e93\u6587\u4ef6\u548chdf5\u8f6f\u4ef6\u4e2d\u7684\u5e93\u6587\u4ef6\r\n$ mkdir bin lib\r\n$ cp blasr bin\/\r\n$ find utils -maxdepth 1 -perm 775 -exec cp {} bin\/ \\;\r\n$ cp .\/libcpp\/pbdata\/libpbdata.so .\/libcpp\/hdf\/libpbihdf.so .\/libcpp\/alignment\/libblasr.so lib\/\r\n$ echo 'export LD_LIBRARY_PATH=\/opt\/sysoft\/hdf5-1.10.0-patch1-linux-centos6-x86_64-gcc447-shared\/lib\/:\/opt\/biosoft\/blasr\/lib\/:$LD_LIBRARY_PATH\r\nPATH=\/opt\/biosoft\/blasr\/bin\/:$PATH' >> ~\/.bashrc.pacbio\r\n$ source ~\/.bashrc.pacbio\r\n<\/pre>\n
\u82e5DBG2OLC\u6d41\u7a0b\u7b2c\u4e09\u6b65\u9009\u62e9\u4f7f\u7528pbdagcon\u8fdb\u884c\u8fd0\u7b97\uff0c\u5219\u9700\u8981\u5b89\u88c5pbdagcon\u8f6f\u4ef6<\/p>\n
\r\npbdagcon\u8f6f\u4ef6\u7684\u7f16\u8bd1\u9700\u8981\u9ad8\u7248\u672cgcc\u652f\u6301\r\n$ git clone https:\/\/github.com\/PacificBiosciences\/pbdagcon.git \/opt\/biosoft\/pbdagcon\r\n$ cd \/opt\/biosoft\/pbdagcon\r\n$ .\/configure.py --boost --gtest --sub --no-pbbam\r\n$ make init-submodule\r\n$ make -j 4\r\n$ make check\r\n$ mkdir bin\r\n$ cp src\/cpp\/dazcon src\/cpp\/pbdagcon bin\/\r\n$ echo 'PATH=\/opt\/biosoft\/pbdagcon\/bin:$PATH' >> ~\/.bashrc.pacbio\r\n$ source ~\/.bashrc.pacbio\r\n<\/pre>\n
3. \u7a0b\u5e8f\u8fd0\u884c<\/h1>\n
\u4f7f\u7528DBG2OLC\u8f6f\u4ef6\u5229\u7528\u4e8c\u4ee3\u548c\u4e09\u4ee3\u6570\u636e\u6df7\u5408\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u5176\u8fd0\u884c\u6d41\u7a0b\u52063\u6b65\u3002<\/p>\n
3.1 \u4f7f\u7528SparseAssembler\u5229\u7528\u4e8c\u4ee3\u6570\u636e\u8fdb\u884cDBG\u7ec4\u88c5<\/h2>\n
\u9996\u5148\uff0c\u5229\u7528Illumina\u5c0f\u7247\u6bb5\u6587\u5e93\u6570\u636e\u4f7f\u7528SparseAssembler\u547d\u4ee4\u7ec4\u88c5\u51facontigs\u5e8f\u5217\u3002\u6b64\u5916\uff0c\u4e5f\u53ef\u4ee5\u4f7f\u7528\u5176\u4ed6\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\u7ec4\u88c5\u51facontigs\u5e8f\u5217\u540e\uff0c\u76f4\u63a5\u8df3\u5230DBG2OLC\u7684\u7b2c\u4e8c\u4e2a\u6b65\u9aa4\u3002\u503c\u5f97\u6ce8\u610f\u7684\u662f\uff1a\u8f93\u5165\u5230\u7b2c\u4e8c\u6b65\u9aa4\u7684contigs\u5fc5\u987b\u662f\u6ca1\u6709\u7ecf\u8fc7repeat resolving\u7684\u539f\u59cb\u5e8f\u5217\uff1b\u7edd\u5927\u90e8\u5206\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\u4e3a\u4e86\u83b7\u5f97\u66f4\u5b8c\u6574\u8fde\u7eed\u7684contigs\u5e8f\u5217\uff0c\u90fd\u727a\u7272\u4e86contigs\u7684\u51c6\u786e\u6027\uff0c\u5176\u7ed3\u679c\u4e0d\u80fd\u7528\u4e8eDBG2OLC\u8f6f\u4ef6\u7684\u7b2c\u4e8c\u6b65\uff0c\u5426\u5219\u6700\u7ec8\u7ed3\u679c\u4f1a\u5f88\u5dee\uff1b\u4f5c\u8005\u63a8\u8350\u53ef\u4ee5\u76f4\u63a5\u7528\u4e8e\u7b2c\u4e8c\u6b65\u7684\u5176\u5b83contig\u7ec4\u88c5\u8f6f\u4ef6\u6709Platanus\u548cMeraculous\u3002
\n\u4e00\u822c\u60c5\u51b5\u4e0b\uff0c\u8f93\u5165\u5230SparseAssembler\u547d\u4ee4\u4e2d~50x\u7684Illumina\u6570\u636e\uff0c\u80fd\u83b7\u5f97\u8f83\u597d\u7684contigs\u7ed3\u679c\u3002
\nSparseAssembler\u547d\u4ee4\u53c2\u6570\uff1a<\/p>\n
\r\n\u5e38\u7528\u53c2\u6570\uff1a\r\nLD \r\n    \u662f\u5426\u8f7d\u5165k-mer graph\u3002\u7b2c\u4e00\u6b21\u8fd0\u884cSparseAssembler\u547d\u4ee4\u7684\u65f6\u5019\uff0c\u8be5\u53c2\u6570\u7684\u503c\u5fc5\u987b\u662f0\uff1b\u82e5\u4e3a\u4e86\u4f7f\u7528SparseAssembler\u5f97\u5230\u66f4\u597d\u7684contigs\u7ed3\u679c\uff0c\u5219\u9700\u8981\u8c03\u6574NodeCovTh\u548cEdgeCovTh\u53c2\u6570\uff1b\u8c03\u6574\u8fd9\u4e9b\u53c2\u6570\u7684\u65f6\u5019\uff0c\u4e0d\u9700\u8981\u518d\u6b21\u8ba1\u7b97k-mer graph\uff0c\u8bbe\u7f6e\u8be5\u53c2\u6570\u4e3a1\u6765\u8df3\u8fc7\u8fd9\u4e2a\u6b65\u9aa4\uff0c\u4ece\u800c\u8282\u7ea6\u5f88\u591a\u65f6\u95f4\u3002\r\nk \r\n  \u8bbe\u7f6e\u4f7f\u7528DBG\u65b9\u6cd5\u8ba1\u7b97\u65f6\u7684Kmer\u5927\u5c0f\uff0c\u652f\u6301\u7684Kmer\u5927\u5c0f\u4e3a15-127\u3002\r\ng \r\n  number of skipped intermediate k-mers, support 1-25.\u8be5\u53c2\u6570\u8f6f\u4ef6\u793a\u4f8b\u4e2d\u4f7f\u7528\u7684\u503c\u662f15\u3002\r\nNodeCovTh \r\n  \u8bbe\u7f6ek-mers\u8986\u76d6\u5ea6\u9608\u503c\uff0c\u53bb\u9664\u8986\u76d6\u5ea6\u8f83\u4f4e\u7684k-mers\u3002\u8be5\u503c\u8bbe\u5b9a\u8303\u56f4\u4e3a0-16\uff0c\u9ed8\u8ba4\u503c\u4e3a1\u3002\r\nEdgeCovTh \r\n  \u8bbe\u7f6elink\u8986\u76d6\u5ea6\u9608\u503c\uff0c\u53bb\u9664\u8986\u76d6\u5ea6\u8f83\u4f4e\u7684links\u3002\u8be5\u503c\u8bbe\u5b9a\u8303\u56f4\u4e3a0-16\uff0c\u9ed8\u8ba4\u503c\u4e3a0\u3002\r\nGS \r\n  \u8bbe\u7f6e\u4e00\u4e2a\u57fa\u56e0\u7ec4\u5927\u5c0f\u7684\u503c\u3002\u8be5\u53c2\u6570\u7528\u4e8e\u51b3\u5b9a\u9884\u5148\u5360\u7528\u7684\u5185\u5b58\u91cf\u3002\u63a8\u8350\u8bbe\u7f6e\u5f97\u6bd4\u57fa\u56e0\u7ec4\u5927\uff0c\u4f8b\u5982\u8bbe\u7f6e\u4e3a2\u500d\u57fa\u56e0\u7ec4\u5927\u5c0f\u3002\r\nf \r\n  \u8f93\u5165\u5355\u7aef\u6d4b\u5e8f\u6570\u636e\u7684\u8def\u5f84\u3002\u8f93\u5165\u6587\u4ef6\u53ef\u4ee5\u662ffasta\u6216fastq\u6587\u4ef6\u3002\u82e5\u6709\u591a\u4e2a\u8f93\u5165\u6587\u4ef6\uff0c\u5219\u4f7f\u7528\u591a\u4e2af\u53c2\u6570\u3002\r\ni1  i2 \r\n  \u8f93\u5165inward paired-end\u6570\u636e\u3002\u82e5\u6709\u591a\u7ec4paired-end\u6570\u636e\uff0c\u5219\u591a\u6b21\u4f7f\u7528i1\/i2\u53c2\u6570\u3002\r\n\r\n\u5176\u5b83\u53c2\u6570\uff1a\r\no1  o2 \r\n  \u8f93\u5165outward paired-end\u6570\u636e\u3002\r\ni1_mp  i2_mp \r\n  \u8f93\u5165\u63d2\u5165\u7247\u6bb5\u957f\u5ea6>10kb\u7684inward paired-end\u6570\u636e\u3002\r\no1_mp  o2_mp \r\n  \u8f93\u5165\u63d2\u5165\u7247\u6bb5\u957f\u5ea6>10kb\u7684outward paired-end\u6570\u636e\u3002\r\nPathCovTh \r\n  \u8bbe\u7f6epath\u8986\u76d6\u5ea6\u9608\u503c\uff0c\u53bb\u9664\u8986\u76d6\u5ea6\u8f83\u4f4e\u7684paths\u3002\u8be5\u503c\u8bbe\u5b9a\u8303\u56f4\u4e3a0-100\u3002\u6839\u636e\u7ecf\u9a8c\uff0c\u4e0d\u63a8\u8350\u6dfb\u52a0\u8be5\u53c2\u6570\u3002\r\nTrimLen \r\n  \u5c06\u6240\u6709\u8fc7\u957f\u7684\u5e8f\u5217\u622a\u77ed\u5230\u6b64\u6307\u5b9a\u7684\u957f\u5ea6\u3002\r\nTrimN \r\n  \u82e5read\u4e2d\u7684\u78b1\u57faN\u6570\u76ee\u8d85\u8fc7\u6b64\u8bbe\u5b9a\u7684\u503c\uff0c\u5219\u53bb\u9664\u8be5read\u6570\u636e\u3002\r\nTrimQual \r\n  \u4ece\u5c3e\u90e8\u622a\u77ed\u8d28\u91cf\u4f4e\u4e8e\u6b64\u503c\u7684\u78b1\u57fa\u3002\r\nQualBase \r\n  \u8bbe\u7f6eFastq\u6587\u4ef6\u4e2d\u6700\u4f4e\u78b1\u57fa\u8d28\u91cf\u5bf9\u5e94\u7684ASCII\u7801\u7b26\u53f7\u3002\u9ed8\u8ba4\u503c\u662f'!'\uff0c\u7b49\u540c\u4e8ePred33\u3002\r\nDenoise \r\n  \u8bbe\u7f6e\u662f\u5426\u5bf9reads\u8fdb\u884c\u4fee\u6b63\u3002\u9ed8\u8ba4\u503c\u662f0\uff0c\u8868\u793a\u4e0d\u5bf9reads\u8fdb\u884c\u4fee\u6b63\u3002\r\nH \r\n  \u6df7\u5408\u6a21\u5f0f\u3002\u9ed8\u8ba4\u503c\u662f0\uff0c\u8868\u793a\u5bf9reads\u7684\u5c3e\u90e8\u8fdb\u884c\u622a\u77ed\uff0c\u6765\u4fdd\u8bc1\u9ad8\u8d28\u91cf\u7684\u6570\u636e\u8fdb\u884creads\u4fee\u6b63\u3002\r\nCovTh \r\n  \u8986\u76d6\u5ea6 < \u6b64\u8bbe\u5b9a\u503c\u7684k-mer\u4f1a\u88ab\u68c0\u6d4b\uff0c\u4ece\u800c\u88ab\u6821\u6b63\u3002\u82e5\u8be5\u53c2\u6570\u503c\u8bbe\u7f6e\u4e3a0\uff0c\u5219\u8f6f\u4ef6\u4f1a\u81ea\u52a8\u8ba1\u7b97\u8be5\u503c\u3002\r\nCorrTh \r\n  \u8986\u76d6\u5ea6 >= \u6b64\u8bbe\u5b9a\u503c\u7684k-mer\u53ef\u4ee5\u7528\u6765\u5bf9reads\u505a\u6821\u6b63\u3002\u82e5\u8be5\u53c2\u6570\u503c\u8bbe\u7f6e\u4e3a0\uff0c\u5219\u8f6f\u4ef6\u4f1a\u81ea\u52a8\u8ba1\u7b97\u8be5\u503c\u3002\r\n<\/pre>\n
SparseAssembler\u8fd0\u884c\u793a\u4f8b\uff1a<\/p>\n
\r\n\u5bf9\u67d0\u7269\u79cdIllumina\u5c0f\u7247\u6bb5\u6587\u5e93\u6d4b\u5e8f\u7684PE150bp\u6570\u636e\u4f7f\u7528trimmomatic\u8d28\u63a7\uff0c\u518d\u4f7f\u7528FindErrors\u8fdb\u884c\u4fee\u6b63\uff0c\u518d\u8fd0\u884cSparseAssembler\uff1a\r\n$ SparseAssembler LD 0 k 95 g 15 NodeCovTh 1 EdgeCovTh 0 GS 60000000 f A.1.fastq f A.2.fastq f B.1.fastq f B.2.fastq\r\n$ cp Contigs.txt Contigs.txt.00\r\n\u589e\u5927NodeCovTh\u548cEdgeCovTh\u53c2\u6570\u540e\uff0c\u518d\u6b21\u8fd0\u884cSparseAssembler\uff0c\u5e76\u6bd4\u8f83\u4e24\u6b21\u7ed3\u679c\u3002\u7b2c\u4e8c\u6b21\u8fd0\u884c\u8f83\u7b2c\u4e00\u6b21\u8fd0\u884c\uff0c\u8017\u65f6\u5c11\u4e86\u5f88\u591a\u5f88\u591a\u3002\r\n$ SparseAssembler LD 1 k 95 g 15 NodeCovTh 2 EdgeCovTh 1 GS 60000000 f A.1.fastq f A.2.fastq f B.1.fastq f B.2.fastq\r\n<\/pre>\n
SparseAssembler\u5728\u5f53\u524d\u76ee\u5f55\u4e0b\u751f\u6210\u4e8618\u4e2a\u6587\u4ef6\u7ed3\u679c\uff0c\u5176\u4e2dContigs.txt\u6587\u4ef6\u662fFasta\u683c\u5f0f\u7684Contigs\u5e8f\u5217\u3002
\n\u8fd0\u884cSparseAssembler\u7684\u6ce8\u610f\u4e8b\u9879\uff1a<\/p>\n
\r\n1. SparseAssembler\u53ea\u53ef\u4ee5\u7b80\u5355\u5730\u5bf9Fastq\u6587\u4ef6\u8fdb\u884c\u8d28\u63a7\u548c\u9519\u8bef\u4fee\u6b63\u3002\u63a8\u8350\u4f7f\u7528\u5176\u5b83\u8f6f\u4ef6\u8fdb\u884creads\u8d28\u63a7\u548c\u4fee\u6b63\uff0c\u4ee5\u83b7\u5f97\u66f4\u597d\u7684\u7ed3\u679c\u3002\r\n2. \u53c2\u6570k\u8bbe\u7f6e\u4e86k-mer\u7684\u5927\u5c0f\uff0c\u8be5\u53c2\u6570\u7684\u503c\u5bf9\u7ed3\u679c\u7684\u5f71\u54cd\u8f83\u5927\u3002\u82e5\u57fa\u56e0\u7ec4\u8f83\u5c0f\uff0c\u63a8\u8350\u8bbe\u7f6e\u591a\u4e2ak-mer\u503c\u8fdb\u884c\u591a\u6b21\u8ba1\u7b97\uff0c\u4ece\u800c\u9009\u62e9\u6700\u4f18k-mer\u503c\u3002\u4e2a\u4eba\u7ecf\u9a8c\uff0cPE150bp\u6570\u636e\u7684\u6700\u4f18\u7684k-mer\u503c\u7ea6\u4e3a91~99\u3002\r\n3. \u9009\u5b9a\u4e86k-mer\u5927\u5c0f\u540e\uff0c\u4f7f\u7528\u9ed8\u8ba4\u7684NodeCovTh\u548cEdgeCovTh\u53c2\u6570\uff08\u9ed8\u8ba4\u53c2\u6570\u4e00\u822c\u80fd\u5f97\u5230\u5f88\u597d\u7684\u7ed3\u679c\uff09\u8fd0\u884c\u4e00\u904dSparseAssembler\u3002\u7136\u540e\u5c1d\u8bd5\u589e\u5927NodeCovTh\u548cEdgeCovTh\u53c2\u6570\uff0c\u8bbe\u7f6eLD 1\u53c2\u6570\u518d\u6b21\u8fd0\u884cSparseAssembler\uff0c\u4ee5\u83b7\u5f97\u6700\u4f18\u7684Contigs\u7ed3\u679c\u3002\r\n4. \u53ef\u80fd\u662f\u5148\u4f7f\u7528\u4e86\u6700\u5c0f\u7684NodeCovTh\u548cEdgeCovTh\u53c2\u6570\u505a\u8fd0\u7b97\u540e\uff0c\u624d\u80fd\u518d\u6b21\u4f7f\u7528\u66f4\u5927\u7684\u53c2\u6570\u8fdb\u884c\u8fd0\u7b97\u3002\r\n5. SparseAssembler\u867d\u7136\u4e5f\u6709\u8f93\u5165\u5927\u7247\u6bb5\u6587\u5e93\u6570\u636e\u7684\u53c2\u6570\u548cScaffolding\u53c2\u6570\uff0c\u4f46\u662f\u4e0d\u63a8\u8350\u8f93\u5165\u5927\u7247\u6bb5\u6587\u5e93\u6570\u636e\u8fdb\u884cScaffolding\u64cd\u4f5c\uff0c\u6ca1\u592a\u5927\u610f\u4e49\u3002\r\n6. \u867d\u7136SparseAssembler\u547d\u4ee4\u7684\u6587\u4ef6\u8f93\u5165\u65b9\u5f0f\u6709\u591a\u79cd\uff0c\u82e5\u662f\u4ec5\u8fdb\u884ccontigs\u7ec4\u88c5\uff0c\u6ca1\u6709\u5229\u7528\u5230paired\u4fe1\u606f\uff0c\u56e0\u6b64\u4f7f\u7528i1 i2\u53c2\u6570\u8f93\u5165\u6587\u4ef6\u548c\u4f7f\u7528f\u53c2\u6570\u8f93\u5165\u6587\u4ef6\u7684\u7ed3\u679c\u662f\u4e00\u6a21\u4e00\u6837\u7684\u3002\r\n<\/pre>\n
3.2 \u4f7f\u7528DBG2OLC\u627eContigs\u5e8f\u5217\u548cPacbio reads\u7684Overlap\u5e76\u8fdb\u884cLayout<\/h2>\n
DBG2OLC\u901a\u8fc7\u6bd4\u8f83contigs\u548cPacbio reads\u4e4b\u95f4\u7684overlap\uff0c\u5c06contigs\u5e8f\u5217\u5b9a\u4f4d\u5230Pacbio reads\u4e0a\uff0c\u5c06DBG\u7684contigs\u7ed3\u679c\u8fd0\u7528\u5230OLC\u7b97\u6cd5\u4e2d\u3002
\nDBG2OLC\u547d\u4ee4\u53c2\u6570\uff1a<\/p>\n
\r\n\u4e3b\u8981\u53c2\u6570\uff1a\r\nLD \r\n  \u662f\u5426\u8f7d\u5165compressed reads information\u3002\u7b2c\u4e00\u6b21\u8fd0\u884cDBG2OLC\u547d\u4ee4\u7684\u65f6\u5019\uff0c\u8be5\u53c2\u6570\u7684\u503c\u5fc5\u987b\u662f0\uff1b\u82e5\u4e3a\u4e86\u5f97\u5230\u66f4\u597d\u7684\u7ed3\u679c\uff0c\u5219\u9700\u8981\u8c03\u6574\u5176\u5b83\u53c2\u6570\uff1b\u8c03\u6574\u8fd9\u4e9b\u53c2\u6570\u7684\u65f6\u5019\uff0c\u8bbe\u7f6e\u8be5\u53c2\u6570\u4e3a1\u6765\u8df3\u8fc7\u8fd9\u4e2a\u6b65\u9aa4\uff0c\u4ece\u800c\u8282\u7ea6\u5f88\u591a\u65f6\u95f4\u3002\r\nk \r\n  \u8bbe\u7f6ek-mer\u5927\u5c0f\u3002k-mer\u7528\u6765\u6bd4\u8f83contig\u548cpacbio read\u4e4b\u95f4\u7684\u91cd\u53e0\uff0c\u800c\u4e0d\u662f\u7528\u4e8e\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u63a8\u8350\u8bbe\u7f6e\u4e3a 17 \u5373\u53ef\u3002\r\nAdaptiveTh \r\n  \u82e5contig\u548cpacbio read\u4e4b\u95f4\u5339\u914d\u7684k-mers\u6570\u76ee < AdaptiveTh * contig\u957f\u5ea6\uff0c\u5219\u8ba4\u4e3acontig\u548cpacbio read\u6ca1\u6709\u91cd\u53e0\u3002\u63a8\u8350\u8bbe\u7f6e\u4e3a0.001-0.02\u3002\r\nKmerCovTh \r\n  \u82e5contig\u548cpacbio read\u4e4b\u95f4\u5339\u914dk-mers\u7684\u8986\u76d6\u5ea6 < KmerCovTh\uff0c\u5219\u8ba4\u4e3acontig\u548cpacbio read\u6ca1\u6709\u91cd\u53e0\u3002\u63a8\u8350\u8bbe\u7f6e\u4e3a2-10\u3002\r\nMinOverlap \r\n  \u4e24\u6761Pacbio read\u4e4b\u95f4\u5339\u914d\u7684k-mers\u6570\u76ee < MinOverlap\uff0c\u5219\u8ba4\u4e3a\u5b83\u4eec\u4e4b\u95f4\u6ca1\u6709\u91cd\u53e0\u3002\u63a8\u8350\u8bbe\u7f6e\u4e3a10-150\u3002\r\nRemoveChimera \r\n  \u53bb\u9664\u5d4c\u5408\u4f53Pacbio reads\u3002\u82e5Pacbio\u6570\u636e\u8986\u76d6\u5ea6\u5927\u4e8e10x\uff0c\u63a8\u8350\u8bbe\u7f6e\u8be5\u53c2\u6570\u4e3a 1 \u3002\r\nContigs \r\n  \u8f93\u5165contigs\u5e8f\u5217\u6587\u4ef6\u8def\u5f84\r\nf \r\n  \u8f93\u5165Pacbio\u6d4b\u5e8fFasta\/Fastq\u6587\u4ef6\u8def\u5f84\u3002\r\n\r\n\u5176\u5b83\u53c2\u6570\uff1a\r\nMinLen \r\n  \u8bbe\u7f6e\u80fd\u7528\u4e8e\u8ba1\u7b97\u7684\u6700\u5c0fPacbio reads\u957f\u5ea6\u3002\r\nChimeraTh \r\n  \u8be5\u53c2\u6570\u9ed8\u8ba4\u503c\u662f 1 \uff1b\u82e5Pacbio\u6570\u636e\u8986\u76d6\u5ea6\u5927\u4e8e100x\uff0c\u5219\u63a8\u8350\u52a0\u5165\u8be5\u53c2\u6570\u5e76\u8bbe\u7f6e\u4e3a 2 \u3002\r\nContigTh \r\n  \u8be5\u53c2\u6570\u9ed8\u8ba4\u503c\u662f 1 \uff1b\u82e5Pacbio\u6570\u636e\u8986\u76d6\u5ea6\u5927\u4e8e100x\uff0c\u5219\u63a8\u8350\u52a0\u5165\u8be5\u53c2\u6570\u5e76\u8bbe\u7f6e\u4e3a 2 \u3002\r\n<\/pre>\n
DBG2OLC\u8fd0\u884c\u793a\u4f8b\uff1a<\/p>\n
\r\n$ DBG2OLC LD 0 k 17 AdaptiveTh 0.001 KmerCovTh 2 MinOverlap 20 RemoveChimera 1 Contigs Contigs.txt f Pacbio_Cell01.fastq f Pacbio_Cell02.fastq\r\n$ DBG2OLC LD 1 k 17 AdaptiveTh 0.005 KmerCovTh 3 MinOverlap 30 RemoveChimera 1 Contigs Contigs.txt f Pacbio_Cell01.fastq f Pacbio_Cell02.fastq\r\n<\/pre>\n
DBG2OLC\u7684\u7ed3\u679c\u6587\u4ef6\u5f88\u591a\uff0c\u5176\u4e3b\u8981\u7ed3\u679c\u6587\u4ef6\u662fbackbone_raw.fasta\u548cDBG2OLC_Consensus_info.txt\uff0c\u662f\u7b2c\u4e09\u6b65\u7684\u8f93\u5165\u6587\u4ef6\u3002
\n\u8fd0\u884cDBG2OLC\u7684\u6ce8\u610f\u4e8b\u9879\uff1a<\/p>\n
\r\n1. AdaptiveTh, KmerCovTh\u548cminOverlap\u8fd93\u4e2a\u8ba1\u7b97Overlap\u7684\u53c2\u6570\u5bf9\u7ed3\u679c\u7684\u5f71\u54cd\u6700\u5927\u3002\u5bf9\u4e8e10x\/20x PacBio\u6570\u636e\uff1aKmerCovTh 2-5, MinOverlap 10-30, AdaptiveTh 0.001~0.01\uff1b\u5bf9\u4e8e50x-100x PacBio\u6570\u636e\uff1aKmerCovTh 2-10, MinOverlap 50-150, AdaptiveTh 0.01-0.02\u3002\r\n2. \u4e0d\u63a8\u8350\u5bf9Pacbio\u6570\u636e\u5c31\u884c\u4fee\u6b63\u540e\u518d\u8fd0\u884cDBG2OLC\u3002\u53ef\u4ee5\u6bd4\u8f83\u4f7f\u7528\u4fee\u6b63\u524d\u7684\u6570\u636e\u7528\u4e8eDBG2OLC\u7684\u7ed3\u679c\uff0c\u4e00\u822c\u60c5\u51b5\u4e0b\u4f7f\u7528\u672a\u4fee\u6b63\u7684Pacbio\u6570\u636e\u80fd\u83b7\u5f97\u66f4\u597d\u7684\u7ed3\u679c\u3002\u6b64\u5916\uff0cDBG2OLC\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u6709\u4e00\u6b65\u591a\u5e8f\u5217\u6bd4\u5bf9\u6a21\u5757\u6765\u8fdb\u884c\u9519\u8bef\u4fee\u6b63\u3002\r\n3. \u53ef\u80fd\u662f\u5148\u4f7f\u7528\u4e86\u6700\u5c0f\u7684AdaptiveTh, KmerCovTh\u548cminOverlap\u53c2\u6570\u505a\u8fd0\u7b97\u540e\uff0c\u624d\u80fd\u518d\u6b21\u4f7f\u7528\u66f4\u5927\u7684\u53c2\u6570\u8fdb\u884c\u8fd0\u7b97\u3002\r\n<\/pre>\n
3.3 Call consensus<\/h2>\n
\u672c\u6b65\u9aa4\u9700\u8981\u4f7f\u7528\/opt\/biosoft\/DBG2OLC\/utility\/\u76ee\u5f55\u4e0b\u7684python\u548cshell\u811a\u672c\uff0c\u6765\u8c03\u7528blasr\u548cconsensus\u6a21\u5757Sparc\uff08\u53ef\u4ee5\u8003\u8651\u4f7f\u7528pbdagcon\u4f5c\u4e3aconsensus\u6a21\u5757\uff0c\u4f46DBG2OLC\u6ca1\u6709\u63d0\u4f9b\u76f8\u5e94\u7684\u811a\u672c\uff09\u8fdb\u884c\u8fd0\u7b97\u3002<\/p>\n
\r\n\u5148\u5c06\/opt\/biosoft\/DBG2OLC\/utility\/\u76ee\u5f55\u4e0b\u7684python\u548cshell\u811a\u672c\u62f7\u8d1d\u5230\u5f53\u524d\u76ee\u5f55\r\n$ cp \/opt\/biosoft\/DBG2OLC\/utility\/*.sh \/opt\/biosoft\/DBG2OLC\/utility\/*.py .\/\r\n\u82e5\u4f7f\u7528\u4e86\u6700\u65b0\u7248\u672c\u7684blasr\u8f6f\u4ef6\uff0c\u5176\u53c2\u6570\u4e66\u5199\u65b9\u6cd5\u6709\u4e00\u4e2a\u4e2d\u5212\u7ebf\u53d8\u6210\u4e86\u4e24\u4e2a\u4e2d\u5212\u7ebf\uff0c\u56e0\u6b64\u9700\u8981\u4fee\u6539.sh\u6587\u4ef6\u4e2dblasr\u547d\u4ee4\u7684\u53c2\u6570\u4e66\u5199\u65b9\u6cd5\u3002\r\n\u6b64\u5916\uff0c\u4e5f\u9700\u8981\u4fee\u6539.sh\u6587\u4ef6\u4e2dSparc\u547d\u4ee4\u8def\u5f84\uff0c\u6216\u8005\u5c06Sparc\u547d\u4ee4\u4e5f\u62f7\u8d1d\u5230\u5f53\u524d\u76ee\u5f55\u3002\r\n\r\n\u5c06Contigs\u5e8f\u5217\u548cPacbio reads\u6570\u636e\u5408\u5e76\u6210\u4e00\u4e2a\u6587\u4ef6ctg_pb.fasta\r\n$ cp Contigs.txt ctg_pb.fasta\r\n$ perl -e 'while (<>) {s\/^\\@\/>\/; print; $_ = <>; print; <>; <>;}' Pacbio_Cell01.fastq >> ctg_pb.fasta\r\n$ perl -e 'while (<>) {s\/^\\@\/>\/; print; $_ = <>; print; <>; <>;}' Pacbio_Cell02.fastq >> ctg_pb.fasta\r\n\r\n\u8fd0\u884c\u811a\u672c\u7a0b\u5e8fsplit_and_run_sparc.sh\r\n$ .\/split_and_run_sparc.sh backbone_raw.fasta DBG2OLC_Consensus_info.txt ctg_pb.fasta .\/ 2 > cns_log.txt\r\n\u7ed3\u679c\u4f1a\u8f93\u51fa\u5230 .\/ \u76ee\u5f55\u4e0b\u3002\u6700\u540e\u7684\u7ed3\u679c\u6587\u4ef6\u662ffinal_assembly.fasta\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. DBG2OLC\u8f6f\u4ef6\u7b80\u4ecb DBG2OLC\u80fd\u5229\u7528\u4e8c\u4ee3\u548c\u4e09\u4ee3\u6df7\u5408\u6570\u636e\u7ec4\u88c5\u5927\u57fa\u56e0\u7ec4 … \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":[3],"tags":[39,40],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2436"}],"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=2436"}],"version-history":[{"count":3,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2436\/revisions"}],"predecessor-version":[{"id":2485,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2436\/revisions\/2485"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2436"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2436"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2436"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}