{"id":2559,"date":"2018-04-24T21:53:43","date_gmt":"2018-04-24T13:53:43","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2559"},"modified":"2019-05-27T10:20:00","modified_gmt":"2019-05-27T02:20:00","slug":"%e4%bd%bf%e7%94%a8nucmer%e8%bf%9b%e8%a1%8c%e5%85%a8%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%ba%8f%e5%88%97%e6%af%94%e5%af%b9","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2559","title":{"rendered":"\u4f7f\u7528nucmer\u8fdb\u884c\u5168\u57fa\u56e0\u7ec4\u5e8f\u5217\u6bd4\u5bf9"},"content":{"rendered":"

1. MUMmer\u7b80\u4ecb<\/h1>\n

MUMmer\uff08Maximal Unique Match mer\uff09\u8f6f\u4ef6\u4e2d\u4f7f\u7528\u7387\u6700\u9ad8\u7684\u547d\u4ee4nucmer\u80fd\u7528\u4e8e\u5bf9\u4e24\u4e2a\u57fa\u56e0\u7ec4assemblies\u8fdb\u884c\u6bd4\u8f83\u3002\u73b0\u5728\u6700\u65b0\u7248\u672c\u7684MUMmer4<\/a>\u76f8\u6bd4\u4e8eMUMmer3<\/a>\uff0c\u80fd\u7528\u4e8e\u66f4\u5927\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u6bd4\u8f83\uff0c\u8fd0\u884c\u901f\u5ea6\u66f4\u5feb\u3002<\/p>\n

2. MUMmer4\u8f6f\u4ef6\u5b89\u88c5<\/h1>\n

\u5148\u5b89\u88c5\u9ad8\u7248\u672cautoconf\u3001automake\u548cyaggo<\/p>\n

$ wget http:\/\/ftp.gnu.org\/gnu\/autoconf\/autoconf-2.69.tar.gz -P ~\/software_packages\/\n$ tar zxf ~\/software_packages\/autoconf-2.69.tar.gz\n$ cd autoconf-2.69\n$ .\/configure --prefix=\/opt\/sysoft\/autoconf-2.69\n$ make -j 24 && make install\n$ echo 'PATH=\/opt\/sysoft\/autoconf-2.69\/bin\/:$PATH' >> ~\/.bashrc\n$ source ~\/.bashrc\n$ cd .. && rm -rf autoconf-2.69\n\n$ wget http:\/\/ftp.gnu.org\/gnu\/automake\/automake-1.16.tar.gz -P ~\/software_packages\/\n$ tar zxf ~\/software_packages\/automake-1.16.tar.gz\n$ cd automake-1.16\n$ .\/configure --prefix=\/opt\/sysoft\/automake-1.16\n$ make -j 24 && make install\n$ echo 'PATH=\/opt\/sysoft\/automake-1.16\/bin\/:$PATH' >> ~\/.bashrc\n$ source ~\/.bashrc\n$ cd .. && rm -rf automake-1.16\n\n$ wget https:\/\/github.com\/gmarcais\/yaggo\/releases\/download\/v1.5.10\/yaggo-1.5.10.tgz -P ~\/software_packages\/\n$ tar zxf ~\/software_packages\/yaggo-1.5.10.tgz -C \/opt\/sysoft\/\n$ make\n$ echo 'PATH=\/opt\/sysoft\/yaggo-1.5.10:$PATH' >> ~\/.bashrc\n$ source ~\/.bashrc\n<\/pre>\n
\u518d\u5b89\u88c5MUMmer4<\/p>\n
$ wget https:\/\/github.com\/mummer4\/mummer\/archive\/v4.0.0beta2.tar.gz -O -P ~\/software_packages\/mummer-4.0.0beta2.tar.gz\n$ tar zxf ~\/software_packages\/mummer-4.0.0beta2.tar.gz\n$ cd mummer-4.0.0beta2\n$ autoreconf -fi\n$ .\/configure --prefix=\/opt\/biosoft\/mummer-4.0.0beta2\n$ source ~\/.bashrc.gcc    \u8981\u4f7f\u7528\u9ad8\u7248\u672cGCC\u8fdb\u884c\u7f16\u8bd1\n$ make -j 24 && make install\n$ cp -r MANUAL.md docs \/opt\/biosoft\/mummer-4.0.0beta2\/\n$ cd .. && rm -rf mummer-4.0.0beta2\n$ cd \/opt\/biosoft\/mummer-4.0.0beta2\/docs\/\n$ latex maxmat3man.tex\n$ dvipdf maxmat3man.dvi\n$ echo 'PATH=$PATH:\/opt\/biosoft\/mummer-4.0.0beta2\/bin\/' >> ~\/.bashrc\n$ source ~\/.bashrc\n<\/pre>\n
\u82e5\u9700\u8981\u4f7f\u7528MUMmer\u8c03\u7528gunplot\u7ed8\u56fe\uff0c\u5219\u9700\u8981\u5b89\u88c5\u9ad8\u7248\u672c\u7684gunplot<\/p>\n
$ wget https:\/\/sourceforge.net\/projects\/gnuplot\/files\/gnuplot\/5.2.2\/gnuplot-5.2.2.tar.gz -P ~\/software_packages\/\n$ tar zxf ~\/software_packages\/gnuplot-5.2.2.tar.gz \n$ cd gnuplot-5.2.2\n$ .\/configure --prefix=\/opt\/sysoft\/gnuplot-5.2.2 && make -j 24 && make install\n$ cd .. && rm -rf gnuplot-5.2.2\n$ echo 'PATH=\/opt\/sysoft\/gnuplot-5.2.2\/bin\/:$PATH' >> ~\/.bashrc\n$ source ~\/.bashrc\n<\/pre>\n
3. mumer\u547d\u4ee4<\/h1>\n
mummer\u547d\u4ee4\u662fMUMmer\u8f6f\u4ef6\u7684\u6838\u5fc3\u7a0b\u5e8f\u3002\u5176\u5b83\u7a0b\u5e8f\uff0c\u5982nucmer\u5c31\u662fperl\u7f16\u5199\u7684\u8c03\u7528\u6b64\u6838\u5fc3\u7a0b\u5e8f\u8fdb\u884c\u6570\u636e\u5206\u6790\u7684\u811a\u672c\u3002\u7531\u4e8e\u8be5\u7a0b\u5e8f\u662f\u6838\u5fc3\u7a0b\u5e8f\uff0cMUMmer\u8f6f\u4ef6\u7ed9\u51fa\u4e86\u8be5\u547d\u4ee4\u7684\u8be6\u7ec6\u8bf4\u660e\u6587\u6863\u3002<\/p>\n
mummer\u547d\u4ee4\u7528\u4e8e\u8ba1\u7b97query assembly\u548creference assembly\u4e2d>=20bp\u7684\u5339\u914d\u5e8f\u5217\uff08maximal matches\uff09\uff0c\u8be5\u6bb5maximal matches\u5e8f\u5217\u5728query\u548creference\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e2d\u5b8c\u5168\u4e00\u81f4\uff0c\u4e14\u5ef6\u957f\u5230\u6700\u957f\u3002<\/p>\n
mumer\u547d\u4ee4\u7684\u4f7f\u7528\uff1a<\/p>\n
mumer\u7528\u6cd5\n$ mummer [options] <ref.fasta> <query1.fasta> [query2.fasta] ...\n    mummer\u53ea\u80fd\u8f93\u5165\u4e00\u4e2areference assembly\u6587\u4ef6\uff0c\u6700\u591a\u652f\u6301\u8f93\u516532\u4e2aquery \nassembly\u6587\u4ef6\u3002\u7a0b\u5e8f\u5c06\u7ed3\u679c\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\u3002\n\u5e38\u7528\u793a\u4f8b\uff1a\n$ mummer -mumreference -l 20 -b -n -c -F ref.fa query.fa > out.txt\n\n\u5e38\u7528\u53c2\u6570\uff1a\n-mum\n-mumreference\n-maxmatch\n    mummer\u7a0b\u5e8f\u7528\u4e8e\u8ba1\u7b97\u83b7\u5f97maximal matches\u3002\u7a0b\u5e8f\u901a\u8fc7suffix array\u7b97\u6cd5\u5c06\nreference assembly\u6784\u5efa\u7d22\u5f15\u6570\u636e\u5e93\uff0c\u7136\u540e\u518d\u5c06query assembly\u548c\u6570\u636e\u5e93\u6bd4\u5bf9\uff0c\n\u641c\u7d22\u5e76\u5f97\u5230maximal matches\u3002\n    \u6709\u5f88\u591amaximal matches\u53ef\u80fd\u5c5e\u4e8e\u91cd\u590d\u5e8f\u5217\uff0c\u800c\u91cd\u590d\u5e8f\u5217\u7684\u6bd4\u5bf9\u53ef\u80fd\u6ca1\u592a\u5927\u610f\u4e49\uff0c\n\u4e14\u91cd\u590d\u5e8f\u5217\u7684\u6bd4\u5bf9\u6781\u5927\u6d88\u8017\u8ba1\u7b97\u91cf\u3002\u56e0\u6b64\uff0c\u9700\u8981\u8003\u8651\u662f\u5426\u9700\u8981\u5f97\u5230\u91cd\u590d\u5e8f\u5217\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\n    \u4ee5\u4e0a3\u4e2a\u53c2\u6570\u5219\u5bf9\u5e94\u91cd\u590d\u5e8f\u5217\u7684\u5904\u7406\u65b9\u6cd5\uff1a\u9ed8\u8ba4\u662f-mumreference\u53c2\u6570\uff0c\u8868\u793a\u6784\u5efa\n\u6570\u636e\u5e93\u65f6\uff0c\u53bb\u6389\u4e86reference assemly\u4e2d\u7684\u91cd\u590d\u5e8f\u5217\uff0c\u5f97\u5230\u7684\u7ed3\u679c\u4e2d\uff0cmaximal \nmatches\u5728reference assembly\u4e2d\u662funique\u7684\uff0c\u8fd9\u79cd\u65b9\u6cd5\u8ba1\u7b97\u901f\u5ea6\u6700\u5feb\uff1b-mum\u53c2\u6570\n\u5219\u662f\u5728\u524d\u8005\u57fa\u7840\u4e0a\uff0c\u5bf9query assembly\u5148\u53bb\u9664\u91cd\u590d\u5e8f\u5217\uff0c\u518d\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5f97\u5230\u7684\u7ed3\u679c\u4e2d\uff0c\nmaximal matches\u5728reference assembly\u548cquery assembly\u4e2d\u90fd\u662funique\u7684\uff0c\n\u8fd9\u79cd\u65b9\u6cd5\u8ba1\u7b97\u901f\u5ea6\u8f83\u6162\uff1b-maxmatch\u53c2\u6570\u5219\u5b8c\u5168\u4e0d\u8003\u8651\u91cd\u590d\u5e8f\u5217\uff0c\u8be5\u65b9\u6cd5\u8ba1\u7b97\u901f\u5ea6\u6700\u6162\uff0c\n\u540c\u65f6\u751f\u6210\u7684\u7ed3\u679c\u6587\u4ef6\u975e\u5e38\u5927\u3002\n\n-l <int>    default: 20\n    \u8bbe\u7f6emaximal match\u7684\u6700\u5c0f\u957f\u5ea6\u3002\n\n-b\n-r\n    \u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0cmummer\u8fdb\u884cmaximal matches\u641c\u7d22\u65f6\uff0c\u8981\u6c42query\u548creference\n\u4e0a\u7684maximal matches\u5e8f\u5217\u5b8c\u5168\u4e00\u81f4\uff1b\u82e5\u52a0\u4e0a-r\u53c2\u6570\uff0c\u5219\u8981\u6c42query\u548creference\n\u4e0a\u7684maximal matches\u5e8f\u5217\u53cd\u5411\u4e92\u8865\uff1b\u82e5\u52a0\u4e0a-b\u53c2\u6570\uff0c\u5219\u4ee5\u4e0a\u4e24\u79cd\u60c5\u51b5\u90fd\u8003\u8651\u3002\n\n-n\n    mummer\u5bf9query\u548creference\u5e8f\u5217\u8fdb\u884c\u6bd4\u8f83\u65f6\uff0c\u80fd\u8bc6\u522b\u4efb\u610f\u5b57\u7b26\uff0c\u4e14\u5bf9\u5b57\u7b26\u5927\u5c0f\u5199\n\u4e0d\u654f\u611f\uff0c\u56e0\u6b64\uff0c\u4e5f\u9002\u5408\u4e8e\u86cb\u767d\u5e8f\u5217\u7684\u6bd4\u8f83\u3002\u82e5\u52a0\u5165\u8be5\u53c2\u6570\uff0c\u5219\u4ec5\u8bc6\u522bATCG\u56db\u79cd\u78b1\u57fa\u5b57\u7b26\uff0c\n\u6240\u6709\u5176\u4ed6\u5b57\u7b26\u90fd\u8ba4\u4e3a\u662f\u4e0d\u80fd\u5339\u914d\u7684\u3002\u9002\u5408\u4e8eassembly\u4e2d\u542b\u6709W\/Y\/N\u7b49\u7b80\u5e76\u78b1\u57fa\u7684\u60c5\u51b5\u3002\n\n-c\n    \u82e5\u52a0\u5165\u53c2\u6570-b\u6216-r\uff0c\u5219\u4f1a\u8003\u8651maximal matches\u5e8f\u5217\u53cd\u5411\u4e92\u8865\u5339\u914d\u7684\u60c5\u51b5\u3002\u8fd9\u65f6\uff0c\nmummer\u5c06query\u5e8f\u5217\u8f6c\u6362\u6210\u53cd\u5411\u4e92\u8865\u5e8f\u5217\uff0c\u5728\u8f93\u51fa\u6587\u4ef6\u4e2d\uff0c>\u4e00\u884c\u540e\u9762\u6709reverse\u5b57\u6837\uff0c\n\u5176\u7ed3\u679c\u4e2d\u7b2c\u4e09\u5217\u7684\u503c\u4e5f\u662f\u8be5\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u7684\u6bd4\u5bf9\u4f4d\u70b9\uff0c\u8868\u793aquery\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u4ece\u8be5\u4f4d\u70b9\n\u5f00\u59cb\u5f80\u540e\u662fmaximal matches\u5e8f\u5217\uff1b\u82e5\u52a0\u5165-c\u53c2\u6570\uff0c\u5219\u5c06\u7b2c\u4e09\u5217\u7684\u503c\u8f6c\u6362\u6210query\u5e8f\u5217\n\u7684\u4f4d\u70b9\uff08query\u5e8f\u5217\u957f\u5ea6 - \u7b2c\u4e09\u5217\u503c + 1\uff09\uff0c\u8868\u793a\u4ece\u8be5\u4f4d\u70b9\u5f80\u524d\u662fmaximal matches\n\u5e8f\u5217\u3002\n\n-F\n    \u7a0b\u5e8f\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0c\u4e00\u822c\u4f1a\u751f\u62104\u5217\u6570\u636e\uff0c\u7b2c\u4e00\u5217\u8868\u793areference\u7684\u5e8f\u5217ID\uff0c\u82e5\nreference\u5e8f\u5217\u4ec5\u6709\u4e00\u6761\uff0c\u5219\u4e0d\u4f1a\u7ed9\u51fa\u8be5\u5217\u6570\u636e\u3002\u52a0\u5165\u8be5\u53c2\u6570\uff0c\u5219\u5f3a\u5236\u6027\u7ed9\u51fa\u8be5\u5217\n\u6570\u636e\u3002<\/pre>\n
mummer\u547d\u4ee4\u7684\u7ed3\u679c\u89e3\u8bfb\uff1a<\/p>\n
1. \u7ed3\u679c\u4e2d>\u5f00\u5934\u884c\u8868\u793a\u67d0\u6761query\u5e8f\u5217\uff0c\u4e4b\u540e\u7684\u884c\u8868\u793a\u8be5\u6761query\u5e8f\u5217\u7684\u8be6\u7ec6\u6bd4\u5bf9\u7ed3\u679c\uff1b\n\u82e5\u8be5\u884c\u6709reverse\uff0c\u5219\u8868\u793a\u8be5query\u5e8f\u5217\u7684\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u7684\u7ed3\u679c\u3002\n2. \u7b2c\u4e00\u5217\u662freference\u5e8f\u5217ID\uff1b\u7b2c\u4e8c\u5217\u8868\u793areference\u8d77\u59cb\u4f4d\u70b9\uff1b\u7b2c\u4e09\u5217\u8868\u793aquery\n\u5e8f\u5217\u6216\u5176\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u7684\u8d77\u59cb\u4f4d\u70b9\uff1b\u7b2c\u56db\u5217\u8868\u793amaximal matches\u5e8f\u5217\u957f\u5ea6\u3002<\/pre>\n
\u5bf9\u4e00\u6bb53000bp\u7684\u5e8f\u5217\u4f5c\u4e3areference\u5e8f\u5217\uff0c\u5bf9\u5176841-1800\u533a\u6bb5\u8fdb\u884c\u53cd\u5411\u4e92\u8865\u540e\uff0c\u4f5c\u4e3a\nquery\u5e8f\u5217\n\n1. \u4e0d\u52a0 -b \u53c2\u6570\uff0c\u5219\u4e0d\u4f1a\u5bf9query\u5e8f\u5217\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u8fdb\u884c\u5206\u6790\n$ mummer -n -F ref.fa query.fa\n> query_seq\n  ref_seq         1         1       840\n  ref_seq      1801      1801      1140\n\n2. \u52a0 -b \u4e0d\u52a0 -c \u53c2\u6570\uff0c\u989d\u5916\u7ed9\u51fa\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u7684\u7ed3\u679c\n$ mummer -b -n -F ref.fa query.fa\n> query_seq\n  ref_seq         1         1       840\n  ref_seq      1801      1801      1140\n> query_seq Reverse\n  ref_seq       841      1141       960\n\u6ce8\u610f Reverse \u8868\u793a\u53cd\u5411\u4e92\u8865\u7ed3\u679c\uff0cquery\u53cd\u5411\u4e92\u8865\u5e8f\u5217\u4ece\u51761141\u4f4d\u70b9\u5f80\u540e\u5171960bp\u5c5e\u4e8e\nmaximal match\u3002\n\n3. \u52a0 -b \u548c -c \u53c2\u6570\n$ mummer -b -c -n -F ref.fa query.fa\n> query_seq\n  ref_seq         1         1       840\n  ref_seq      1801      1801      1140\n> query_seq Reverse\n  ref_seq       841      1800       960\n\n\u6ce8\u610f Reverse \u8868\u793a\u53cd\u5411\u4e92\u8865\u7ed3\u679c\uff0cquery\u5e8f\u5217\u4ece\u51761800\u4f4d\u70b9\u5f80\u524d960bp\u5c5e\u4e8emaximal \nmatch\u3002<\/pre>\n
4. nucmer\u547d\u4ee4<\/h1>\n
nucmer\u547d\u4ee4\u7528\u4e8e\u5bf9nucleotide\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\u3002\u76f8\u6bd4\u4e8emummer\u547d\u4ee4\uff0cnucmer\u547d\u4ee4\u80fd\u5c06\u76f8\u90bb\u7684maximal matches\u8fde\u8d77\u6765\u4f5c\u4e3acluster\uff0c\u7136\u540e\u5bf9cluster\u4e24\u7aef\u8fdb\u884c\u5ef6\u4f38\uff0c\u5f62\u6210\u5927\u7684\u5339\u914d\u533a\u57df\uff1b\u5e76\u4e14\u8ba1\u7b97SNP\u6570\u91cf\u548cINDEL\u95f4\u7684\u8ddd\u79bb\u3002<\/p>\n
nucmer\u547d\u4ee4\u662fMUMmer\u8f6f\u4ef6\u4f7f\u7528\u6700\u591a\u7684\u547d\u4ee4\uff0c\u5e38\u7528\u4e8e\u76f8\u4f3c\u6027\u5f88\u9ad8\u7684\u6838\u9178\u5e8f\u5217\u6bd4\u8f83\uff0c\u7279\u522b\u662f\u901a\u4e00
\n\u4e2a\u7269\u79cd\u95f4\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u6bd4\u8f83\uff0c\u6216\u4e0d\u540cDe novo\u7ec4\u88c5\u8f6f\u4ef6\u5f97\u5230\u7684assemblies\u4e4b\u95f4\u7684\u6bd4\u8f83\u3002<\/p>\n
nucmer\u547d\u4ee4\u7684\u4f7f\u7528\uff1a<\/p>\n
\u7528\u6cd5\u548c\u5e38\u7528\u793a\u4f8b\uff1a\n$ nucmer [options] ref:path query:path\n\n$ nucmer -c 200 -g 200 ref.fa query.fa\n\u5e38\u7528\u53c2\u6570\uff1a\n-p <string>    default: out\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u524d\u7f00\u3002\n--num\n--mumreference\n--maxmatch\n    mummer\u7a0b\u5e8f\u7528\u4e8e\u8ba1\u7b97\u83b7\u5f97maximal matches\u3002\u7a0b\u5e8f\u901a\u8fc7suffix array\u7b97\u6cd5\u5c06\nreference assembly\u6784\u5efa\u7d22\u5f15\u6570\u636e\u5e93\uff0c\u7136\u540e\u518d\u5c06query assembly\u548c\u6570\u636e\u5e93\u6bd4\u5bf9\uff0c\n\u641c\u7d22\u5e76\u5f97\u5230maximal matches\u3002\n    \u6709\u5f88\u591amaximal matches\u53ef\u80fd\u5c5e\u4e8e\u91cd\u590d\u5e8f\u5217\uff0c\u800c\u91cd\u590d\u5e8f\u5217\u7684\u6bd4\u5bf9\u53ef\u80fd\u6ca1\u592a\u5927\u610f\u4e49\uff0c\n\u4e14\u91cd\u590d\u5e8f\u5217\u7684\u6bd4\u5bf9\u6781\u5927\u6d88\u8017\u8ba1\u7b97\u91cf\u3002\u56e0\u6b64\uff0c\u9700\u8981\u8003\u8651\u662f\u5426\u9700\u8981\u5f97\u5230\u91cd\u590d\u5e8f\u5217\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\n    \u4ee5\u4e0a3\u4e2a\u53c2\u6570\u5219\u5bf9\u5e94\u91cd\u590d\u5e8f\u5217\u7684\u5904\u7406\u65b9\u6cd5\uff1a\u9ed8\u8ba4\u662f-mumreference\u53c2\u6570\uff0c\u8868\u793a\u6784\u5efa\n\u6570\u636e\u5e93\u65f6\uff0c\u53bb\u6389\u4e86reference assemly\u4e2d\u7684\u91cd\u590d\u5e8f\u5217\uff0c\u5f97\u5230\u7684\u7ed3\u679c\u4e2d\uff0cmaximal \nmatches\u5728reference assembly\u4e2d\u662funique\u7684\uff0c\u8fd9\u79cd\u65b9\u6cd5\u8ba1\u7b97\u901f\u5ea6\u6700\u5feb\uff1b-mum\u53c2\u6570\n\u5219\u662f\u5728\u524d\u8005\u57fa\u7840\u4e0a\uff0c\u5bf9query assembly\u5148\u53bb\u9664\u91cd\u590d\u5e8f\u5217\uff0c\u518d\u8fdb\u884c\u6bd4\u5bf9\uff0c\u5f97\u5230\u7684\u7ed3\u679c\u4e2d\uff0c\nmaximal matches\u5728reference assembly\u548cquery assembly\u4e2d\u90fd\u662funique\u7684\uff0c\n\u8fd9\u79cd\u65b9\u6cd5\u8ba1\u7b97\u901f\u5ea6\u8f83\u6162\uff1b-maxmatch\u53c2\u6570\u5219\u5b8c\u5168\u4e0d\u8003\u8651\u91cd\u590d\u5e8f\u5217\uff0c\u8be5\u65b9\u6cd5\u8ba1\u7b97\u901f\u5ea6\u6700\u6162\uff0c\n\u540c\u65f6\u751f\u6210\u7684\u7ed3\u679c\u6587\u4ef6\u975e\u5e38\u5927\u3002\n    nucmer\u547d\u4ee4\u8c03\u7528mummer\u7a0b\u5e8f\u8fdb\u884c\u8ba1\u7b97\uff0c\u6cbf\u7528\u4e86\u4ee5\u4e0a3\u4e2a\u53c2\u6570\uff0c\u53ea\u662f\u53c2\u6570\u7684\u4f7f\u7528\u7531\n\u4e00\u4e2a\u4e2d\u5212\u7ebf\u53d8\u6210\u4e86\u4e24\u4e2a\u4e2d\u5212\u7ebf\u3002\n    \u82e5\u6bd4\u8f83\u4e24\u4e2a\u57fa\u56e0\u7ec4\uff0c\u5e0c\u671b\u5f97\u5230\u66f4\u5927\u7684\u6bd4\u5bf9\u533a\u57df\uff0c\u5219\u8003\u8651\u4f7f\u7528--maxmatch\u53c2\u6570\uff1b\u82e5\n\u60f3\u6574\u5408\u4e24\u4e2aassemblies\uff0c\u5219\u6700\u597d\u4e0d\u5bf9\u91cd\u590d\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9\uff0c\u8003\u8651\u4f7f\u7528--mumreference\n\u53c2\u6570\u3002\n\n-f | --forward\n-r | --reverse\n    \u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\uff0c\u7a0b\u5e8f\u5bf9\u6b63\u8d1f\u94fe\u90fd\u8fdb\u884c\u6bd4\u5bf9\uff1b\u52a0\u5165-f\u53c2\u6570\u5219\u4ec5\u5bf9\u6b63\u94fe\u8fdb\u884c\u6bd4\u5bf9\uff1b\u52a0\u5165-r\n\u53c2\u6570\u5219\u4ec5\u5bf9\u8d1f\u94fe\u8fdb\u884c\u6bd4\u5bf9\u3002\n\n-l <int>    default: 20\n    \u8bbe\u7f6emaximal match\u7684\u6700\u5c0f\u957f\u5ea6\u3002\n\n-g <int>    default: 90\n    \u5c06\u4e24\u4e2a\u76f8\u90bb\u7684maximal matches\u8fde\u8d77\u6765\uff0c\u4f5c\u4e3a\u4e00\u4e2acluster\uff0c\u8981\u6c42\u8fd9\u4e24\u4e2amatches\n\u4e4b\u95f4\u7684\u8ddd\u79bb\u4e0d\u8d85\u8fc7\u8be5\u53c2\u6570\u6307\u5b9a\u7684\u78b1\u57fa\u6570\u3002\n\n-c <int>    default: 65\n    \u4e00\u4e2acluster\u4e2d\u6240\u6709maximal matches\u7684\u957f\u5ea6\u603b\u548c\u8981\u4e0d\u5c0f\u4e8e\u8be5\u53c2\u6570\u503c\u3002\n\n-d <float>    default: .12\n-D <int>    default: 5\n    \u82e5cluster\u4e2d\u76f8\u90bb\u7684\u4e24\u4e2amaximal matches\u548c\u4e2d\u95f4Gap\u533a\u6bb5\u4e2d\uff0c\u53d8\u5f02\u7684\u78b1\u57fa\u6bd4\u7387\n\u8981\u4f4e\u4e8e-d\u53c2\u6570\u503c\uff1b\u53d8\u5f02\u7684\u4e2a\u6570\u8981\u5c11\u4e8e-D\u53c2\u6570\u503c\u3002\n--extend\n--noextend\n    \u8bbe\u7f6e\u662f\u5426\u5bf9clustering\u4e24\u7aef\u8fdb\u884c\u5ef6\u4f38\u3002\u9ed8\u8ba4\u8bbe\u7f6e\u662f--extend\u3002\n\n-b <int>    default: 200\n    \u5bf9cluster\u4e24\u7aef\u8fdb\u884c\u5ef6\u4f38\uff08cluster\u4fa7\u7ffc\u5b58\u5728\u4e00\u5b9a\u957f\u5ea6\u7684\u5339\u914d\u533a\u57df\uff09\u65f6\uff0c\u4e0d\u80fd\u8de8\u8d8a\n\u957f\u5ea6\u8d85\u8fc7200bp\u7684\u4f4e\u5339\u914d\u5f97\u5206\u533a\u57df\u3002\n\n-t | --threads <int>    \n    \u8bbe\u7f6e\u7a0b\u5e8f\u8fd0\u884c\u6240\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\u3002\u9ed8\u8ba4\u503c\u662f\u4f7f\u7528\u8ba1\u7b97\u673a\u6240\u6709CPU\u7ebf\u7a0b\u6570\u3002nucmer\u591a\n\u7ebf\u7a0b\u6548\u7387\u4e0d\u9ad8\uff1a\u4f8b\u5982\uff0c80\u7ebf\u7a0b\u670d\u52a1\u5668\u8fd0\u884c\u4e00\u4e2anucmer\u547d\u4ee4\uff0c\u5e73\u5747\u8d1f\u8f7d\u4e0d\u523040\uff0c\u771f\u5b9e\u7684\nCPU\u7ebf\u7a0b\u8d44\u6e90\u6d88\u8017\u4e0d\u523020\u3002\n\n--save <string>\n    \u52a0\u5165\u8be5\u53c2\u6570\uff0c\u5219\u80fd\u751f\u6210reference\u5e8f\u5217\u7684\u7d22\u5f15\u6570\u636e\u5e93\uff0c\u8be5\u53c2\u6570\u503c\u662f\u751f\u6210\u7684\u7d22\u5f15\u6570\n\u636e\u5e93\u6587\u4ef6\u524d\u7f00\u3002\n\n--load <string>\n    \u8f93\u5165reference\u7d22\u5f15\u6570\u636e\u5e93\u524d\u7f00\u3002\u4f7f\u7528\u524d\u4e00\u4e2a\u53c2\u6570\u548c\u6b64\u53c2\u6570\uff0c\u5728\u591a\u6b21\u5229\u7528nucmer\n\u547d\u4ee4\u8fdb\u884c\u5206\u6790\u65f6\uff0c\u80fd\u8282\u7ea6\u8ba1\u7b97\u65f6\u95f4\u3002<\/pre>\n
nucmer\u7a0b\u5e8f\u8f93\u51fa\u6587\u4ef6\u4e3aout.delta\u3002\u8be5\u6587\u4ef6\u793a\u4f8b\u5185\u5bb9\uff1a<\/p>\n
\/home\/username\/reference.fasta \/home\/username\/query.fasta\nNUCMER\n>ref_seq1 query_seq1 500 2000000\n88 198 1641558 1641668 0 0 0\n0\n167 4877 1 4714 15 15 0\n2456\n1\n-11\n769\n950\n1\n1\n-142\n-1\n0\n>ref_seq2 query_seq4 50000 30000\n5198 22885 5389 23089 18 18 0\n-6\n-32\n-1\n-1\n-1\n7\n1130\n0\n<\/pre>\n
out.delta\u6587\u4ef6\u683c\u5f0f\u89e3\u6790\uff1a<\/p>\n
1. \u6587\u4ef6\u7b2c\u4e00\u884c\u662f\u4e24\u4e2a\u9700\u8981\u6bd4\u8f83\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217fasta\u6587\u4ef6\u7684\u7edd\u5bf9\u8def\u5f84\u3002\n2. \u7b2c\u4e8c\u884c\u662f\u6bd4\u5bf9\u7c7b\u578b\uff0c\u53ef\u4ee5\u662fNUCMER\u6216PROMER\u3002\n3. \u7b2c\u4e09\u884c\u5f80\u540e\u662f\u6bd4\u5bf9\u7ed3\u679c\u3002\u6bcf\u4e2a\u6bd4\u5bf9\u7ed3\u679c\u4ee5\u884c\u9996\u4e3a > \u53f7\u5f00\u5934\uff0c\u6574\u884c\u4e3a 0 \u7ed3\u5c3e\u3002\n4. \u6bd4\u5bf9\u7ed3\u679c\u7b2c\u4e00\u884c\u4ee5 > \u53f7\u5f00\u5934\uff0c\u540e\u9762\u5305\u542b\u7a7a\u683c\u5206\u5272\u76844\u5217\uff0c\u5206\u522b\u662f\uff1areference\u5e8f\u5217\n   ID\u3001query\u5e8f\u5217ID\u3001\u8be5reference\u5e8f\u5217\u957f\u5ea6\u3001\u8be5query\u5e8f\u5217\u957f\u5ea6\u3002\n5. \u6bd4\u5bf9\u7ed3\u679c\u7b2c\u4e8c\u884c\u5305\u542b\u7a7a\u683c\u5206\u5272\u76847\u5217\u6570\u503c\uff0c\u5206\u522b\u662f\uff1areference\u5e8f\u5217\u6bd4\u5bf9\u8d77\u59cb\u4f4d\u70b9\u3001\n   reference\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u675f\u4f4d\u70b9\u3001query\u5e8f\u5217\u6bd4\u5bf9\u8d77\u59cb\u4f4d\u70b9\u3001query\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u675f\u4f4d\n   \u70b9\u3001\u9519\u914d\u4f4d\u70b9\u6570\u3001\u4e0d\u76f8\u4f3c\u4f4d\u70b9\u6570\uff08\u5728\u86cb\u767d\u5e8f\u5217\u6bd4\u5bf9\u4e2d\u6709\u610f\u4e49\uff0c\u6838\u9178\u5e8f\u5217\u6bd4\u5bf9\u4e2d\u548c\u524d\n   \u4e00\u4e2a\u6570\u503c\u4e00\u81f4\uff09\u3001\u975e\u5b57\u6bcd\u5b57\u7b26\u4e2a\u6570\uff08\u5728\u86cb\u767d\u5e8f\u5217\u6bd4\u5bf9\u4e2d\u8868\u793a\u7ec8\u6b62\u5bc6\u7801\u5b50\u4e2a\u6570\uff0c\u5728\u6838\n   \u9178\u5e8f\u5217\u6bd4\u5bf9\u4e2d\u4e00\u822c\u662f0\uff09\n6. \u7b2c\u4e09\u884c\u5f80\u540e\u662fDelta\u503c\uff0c\u8868\u793a\u79bb\u4e0b\u4e00\u4e2aIDNEL\u4e4b\u95f4\u7684\u8ddd\u79bb\uff0c\u6b63\u6570\u8868\u793a\u5728reference\n   \u4e2d\u662fInserion\uff0c\u8d1f\u6570\u8868\u793a\u5728reference\u4e2d\u662fDeletion\u3002\u6700\u540e\u4e00\u884c\u662f0\u3002\n   \u4f8b\u5982\uff1a reference  acg.tagctgag$\n             query  .cggtag.tgag$\n   Delta = (1, -3, 4, 0)\u3002<\/pre>\n
5. promer\u547d\u4ee4<\/h1>\n
promer\u547d\u4ee4\u548cnucmer\u547d\u4ee4\u7c7b\u4f3c\uff0c\u4e0d\u8fc7\u4f1a\u5c06\u6838\u9178\u5e8f\u5217\u7ffb\u8bd1\u62106\u4e2a\u8bfb\u7801\u6846\u540e\uff0c\u5728\u86cb\u767d\u6c34\u5e73\u8fdb\u884c\u6bd4\u5bf9\uff0c\u4ece\u800c\u9002\u5408\u4e8e\u6838\u9178\u6c34\u5e73\u4e0a\u76f8\u4f3c\u6027\u8f83\u4f4e\uff0c\u86cb\u767d\u6c34\u5e73\u4e0a\u76f8\u4f3c\u6027\u8f83\u9ad8\u7684\u6838\u9178\u5e8f\u5217\u6bd4\u5bf9\u3002<\/p>\n
promer\u76f8\u5bf9\u4f7f\u7528\u8f83\u5c11\uff0c\u662f\u4f7f\u7528\u53c2\u6570\u548cnucmer\u57fa\u672c\u4e00\u81f4\u3002<\/p>\n
6. delta-filter\u547d\u4ee4<\/h1>\n
delta-filter\u547d\u4ee4\u80fd\u5bf9nucmer\u6216promer\u7684\u7ed3\u679c\u6587\u4ef6\u8fdb\u884c\u8fc7\u6ee4\uff0c\u53bb\u9664\u4f4e\u8d28\u91cf\u7684\u5339\u914d\u533a\u57df\u3002\u5176
\n\u4f7f\u7528\u65b9\u6cd5\uff1a<\/p>\n
\u7528\u6cd5\uff1a\n$ delta-filter [options] <deltafile>\n\n\u5e38\u7528\u793a\u4f8b\uff1a\n$ delta-filter -i 90 -l 2000 -m out.delta > out.f.delta\n\n\u5e38\u7528\u53c2\u6570\uff1a\n-i <float>    default\uff1a 0\n    \u8be5\u53c2\u6570\u7684\u503c\u5fc5\u987b\u8bbe\u5b9a\u4e3a0~100\uff0c\u8868\u793a\u8fc7\u6ee4\u6389Identity\u4f4e\u4e8e\u6b64\u503c\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\n\n-l <float>    default: 0\n    \u8fc7\u6ee4\u6389\u5339\u914d\u533a\u57df\u957f\u5ea6\u4f4e\u4e8e\u6b64\u503c\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\n\n-u <float>    default: 0\n    \u8981\u6c42\u6bd4\u5bf9\u533a\u57df\u7684unique\u5e8f\u5217\u6240\u5360\u7684\u767e\u5206\u6bd4\u4e0d\u4f4e\u4e8e\u6b64\u503c\u3002\n\n-q\n    \u5bf9query\u5e8f\u5217\u7684\u6bcf\u4e2a\u6bd4\u5bf9\u4f4d\u70b9\uff0c\u4ec5\u9009\u62e9\u5176\u5728reference\u5e8f\u5217\u4e0a\u7684\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\u3002\n\u82e5\u9700\u8981\u5c06contigs\u5e8f\u5217\u6216reads\u5b9a\u4f4d\u5230reference genome\u4e0a\uff0c\u8003\u8651\u4f7f\u7528-q\u53c2\u6570\u3002\n\n-r\n    \u5bf9reference\u5e8f\u5217\u7684\u6bcf\u4e2a\u6bd4\u5bf9\u4f4d\u70b9\uff0c\u4ec5\u9009\u62e9\u5176\u5728query\u5e8f\u5217\u7684\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\u3002\n\n-g\n    \u52a0\u5165\u8be5\u53c2\u6570\uff0c\u5219\u8981\u6c42\u6bd4\u5bf9\u533a\u57df\u5185\u90e8\u7684maximal matches\u4e4b\u95f4\u4e0d\u80fd\u6709\u91cd\u6392\uff0c\u5982\n\u79fb\u4f4d\u3001\u5012\u4f4d\u7b49\u3002\n \n-m\n    \u52a0\u5165\u8be5\u53c2\u6570\uff0c\u8868\u793a\u53d6-q\u548c-r\u53c2\u6570\u7684\u5e76\u96c6\u3002\u4e00\u4e2aquery\u4f4d\u70b9\u53ef\u80fd\u6bd4\u5bf9\u5230ref\u4e0a\u591a\n\u4e2a\u4f4d\u70b9\uff0c\u4ec5\u4fdd\u7559\u5176\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\uff1b\u4e00\u4e2aref\u4f4d\u70b9\u4e5f\u53ef\u80fd\u6bd4\u5bf9\u5230query\u4e0a\u591a\u4e2a\u4f4d\u70b9\uff0c\u4ec5\n\u4fdd\u7559\u5176\u6700\u4f18\u6bd4\u5bf9\u7ed3\u679c\uff1b\u4ee5\u4e0a\u4e24\u4e2a\u5904\u7406\u65b9\u6cd5\u7684\u8f93\u5165\u4fe1\u606f\u662f\u4e00\u6837\u7684\uff0c\u90fd\u662f\u6240\u6709\u7684\u6bd4\u5bf9\u7ed3\u679c\uff1b\n\u82e5\u4f7f\u7528 -q -r \u53c2\u6570\uff0c\u5219\u662f\u5148\u8fd0\u7528\u7b2c\u4e00\u79cd\u65b9\u6cd5\u5904\u7406\uff0c\u5f97\u5230\u7684\u7ed3\u679c\u518d\u8fd0\u7528\u7b2c\u4e8c\u79cd\u65b9\u6cd5\n\u5904\u7406\uff0c\u5176\u7ed3\u679c\u76f8\u6bd4\u4e8e\u4ec5\u4f7f\u7528 -m \u53c2\u6570\uff0c\u8f93\u51fa\u7684\u6bd4\u5bf9\u7ed3\u679c\u66f4\u5c11\u3002\u4e00\u822c\u60c5\u51b5\u4e0b\uff0c\u4f7f\u7528 -m\n\u53c2\u6570\u662f\u6700\u4f18\u7684\u65b9\u6cd5\u3002\n\n-1\n    \u52a0\u5165\u8be5\u53c2\u6570\uff0c\u8868\u793a\u53d6-q\u548c-r\u53c2\u6570\u7684\u4ea4\u96c6\u3002\u4e00\u4e2aquery\u4f4d\u70b9\u53ef\u80fd\u6bd4\u5bf9\u5230ref\u4e0a\u591a\n\u4e2a\u4f4d\u70b9\uff0c\u4e00\u4e2aref\u4f4d\u70b9\u4e5f\u53ef\u80fd\u6bd4\u5bf9\u5230query\u4e0a\u591a\u4e2a\u4f4d\u70b9\uff1b\u52a0\u5165\u8be5\u53c2\u6570\uff0c\u8868\u793a\u8981\u6c42query\n\u4f4d\u70b9\u548cref\u4f4d\u70b9\u80fd\u76f8\u4e92\u6bd4\u5bf9\u4e0a\uff0c\u4e14\u5b83\u4eec\u662f\u76f8\u4e92\u6700\u4f73\u6bd4\u5bf9\uff1b\u82e5\u4f7f\u7528 -q -r \u53c2\u6570\uff0c\u5f97\u5230\u7684\n\u867d\u7136\u4e5f\u662f1\u5bf91\u7684\u6bd4\u5bf9\u7ed3\u679c\uff0c\u4f46\u5176\u4e0d\u4e00\u5b9a\u662f\u76f8\u4e92\u6700\u4f73\u6bd4\u5bf9\uff0c-1\u53c2\u6570\u7684\u8f93\u51fa\u5bf9\u7ed3\u679c\u66f4\u5c11\u3002\n\u82e5\u9700\u8981\u5f97\u5230SNP\u7ed3\u679c\uff0c\u5219\u9700\u8981\u52a0\u5165\u8be5\u53c2\u6570\u6765\u786e\u4fdd\u7ed3\u679c\u7684\u51c6\u786e\u6027\u3002\n\ndelta-filter\u5bf9\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884c\u8fc7\u6ee4\u65f6\uff0c\u6709\u591a\u79cd\u8fc7\u6ee4\u53c2\u6570\uff0c\u8fc7\u6ee4\u987a\u5e8f\u662f\uff1a-i -l -u\n-q -r -g -m -1\u3002\n<\/pre>\n
7. dnadiff\u547d\u4ee4<\/h1>\n","protected":false},"excerpt":{"rendered":"
1. MUMmer\u7b80\u4ecb MUMmer\uff08Maximal Unique Match  … \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\/2559"}],"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=2559"}],"version-history":[{"count":18,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2559\/revisions"}],"predecessor-version":[{"id":2916,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2559\/revisions\/2916"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2559"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2559"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2559"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}