{"id":2270,"date":"2015-08-25T16:26:27","date_gmt":"2015-08-25T08:26:27","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2270"},"modified":"2015-08-25T16:26:34","modified_gmt":"2015-08-25T08:26:34","slug":"pbjelly2%e5%88%a9%e7%94%a8pacbio%e6%95%b0%e6%8d%ae%e8%bf%9b%e8%a1%8cscaffolding","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2270","title":{"rendered":"PBJelly2\u5229\u7528Pacbio\u6570\u636e\u8fdb\u884cscaffolding"},"content":{"rendered":"

1.PBJelly2 \u7b80\u4ecb<\/h1>\n

PBJelly2<\/a> \u7528\u4e8e\u5229\u7528 Pacbio \u6570\u636e\u8fdb\u884c\u57fa\u56e0\u7ec4\u8865\u6d1e\u548c scaffold \u8fde\u63a5\u3002<\/p>\n

2.\u5b89\u88c5 PBJelly2 <\/h1>\n
\r\n\u5b89\u88c5 HDF<\/a>\uff1a\r\n$ wget http:\/\/www.hdfgroup.org\/ftp\/HDF5\/current\/bin\/linux-centos6-x86_64\/hdf5-1.8.15-patch1-linux-centos6-x86_64-shared.tar.gz\r\n$ tar zxf hdf5-1.8.15-patch1-linux-centos6-x86_64-shared.tar.gz\r\n$ mv hdf5-1.8.15-patch1-linux-centos6-x86_64-shared \/opt\/biosoft\/hdf5-1.8.15-patch1\r\n$ export HDF5INCLUDEDIR=\/opt\/biosoft\/hdf5-1.8.15-patch1\/include\/\r\n$ export HDF5LIBDIR=\/opt\/biosoft\/hdf5-1.8.15-patch1\/lib\/\r\n$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\/opt\/biosoft\/hdf5-1.8.15-patch1\/lib\/\r\n$ export C_INCLUDE_PATH=$C_INCLUDE_PATH:\/opt\/biosoft\/hdf5-1.8.15-patch1\/include\/\r\n\r\n\u5b89\u88c5 Blasr<\/a>\uff08\u9700\u6c42 HDF v1.8.0\u6216\u4ee5\u4e0a\u7248\u672c\uff09\uff1a\r\n$ wget https:\/\/github.com\/PacificBiosciences\/blasr\/archive\/master.zip -O blasr.zip\r\n$ unzip blasr.zip\r\n$ mv blasr-master\/ \/opt\/biosoft\/blasr\r\n$ cd \/opt\/biosoft\/blasr\r\n$ make -j 8\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/blasr\/alignment\/bin\/' >> ~\/.bashrc\r\n\r\n\u5b89\u88c5Python\u6a21\u5757 Networkx v1.7\r\n$ wget https:\/\/pypi.python.org\/packages\/source\/n\/networkx\/networkx-1.7.tar.gz\r\n$ tar zxf networkx-1.7.tar.gz\r\n$ cd networkx-1.7\r\n$ sudo \/usr\/local\/bin\/python setup.py install\r\n\r\n\u5b89\u88c5Python\u6a21\u5757 pyparsing\r\n$ wget https:\/\/pypi.python.org\/packages\/source\/p\/pyparsing\/pyparsing-2.0.3.tar.gz\r\n$ tar zxf pyparsing-2.0.3.tar.gz\r\n$ cd pyparsing-2.0.3\r\n$ sudo \/usr\/local\/bin\/python setup.py install\r\n\r\n\u5b89\u88c5Python\u6a21\u5757 numpy\r\n$ wget https:\/\/pypi.python.org\/packages\/source\/n\/numpy\/numpy-1.9.2.tar.gz\r\n$ tar zxf numpy-1.9.2.tar.gz \r\n$ cd numpy-1.9.2\r\n$ sudo \/usr\/local\/bin\/python setup.py install\r\n\r\n\u5b89\u88c5Python\u6a21\u5757 h5py\r\n$ wget https:\/\/pypi.python.org\/packages\/source\/h\/h5py\/h5py-2.5.0.tar.gz\r\n$ cd h5py-2.5.0\r\n$ export LIBRARY_PATH=\/opt\/biosoft\/hdf5-1.8.15-patch1\/lib\/:$LIBRARY_PATH\r\n$ \/usr\/local\/bin\/python setup.py build\r\n$ sudo \/usr\/local\/bin\/python setup.py install\r\n\r\n\u5b89\u88c5Python\u6a21\u5757 pysam\r\n$ https:\/\/pypi.python.org\/packages\/source\/p\/pysam\/pysam-0.8.3.tar.gz\r\n$ tar zxf pysam-0.8.3.tar.gz \r\n$ cd pysam-0.8.3\r\n$ sudo \/usr\/local\/bin\/python setup.py install\r\n\r\n\u5b89\u88c5Python\u6a21\u5757 intervaltree\r\n$ wget https:\/\/pypi.python.org\/packages\/source\/i\/intervaltree\/intervaltree-2.0.4.tar.gz\r\n$ tar zxf intervaltree-2.0.4.tar.gz\r\n$ cd intervaltree-2.0.4\r\n$ sudo \/usr\/local\/bin\/python setup.py install\r\n\r\n\u5b89\u88c5 PBJelly2\r\n$ wget http:\/\/sourceforge.net\/projects\/pb-jelly\/files\/latest\/download -O PBSuite.tar.gz\r\n$ tar zxf PBSuite.tar.gz -C \/opt\/biosoft\/\r\n$ SWEETPATH=`ls \/opt\/biosoft\/PBSuite* -d`\r\n$ echo \"perl -p -i -e 's#export SWEETPATH=.*#export SWEETPATH=$SWEETPATH#' $SWEETPATH\/setup.sh\" | sh\r\n$ echo \"source $SWEETPATH\/setup.sh\" >> ~\/.bashrc\r\n<\/pre>\n
3. \u4f7f\u7528 PBJelly2 \u8fdb\u884c\u8865\u6d1e<\/h1>\n
\u9996\u5148\u521b\u5efa\u914d\u7f6e\u6587\u4ef6 Protocol.xml\uff0c\u5185\u5bb9\u5982\u4e0b:<\/p>\n
\r\n<jellyProtocol>\r\n    <reference>\u57fa\u56e0\u7ec4fasta\u6587\u4ef6\u7684\u8def\u5f84<\/reference>  \r\n    <outputDir>\u8f93\u51fa\u6587\u4ef6\u8def\u5f84<\/outputDir>\r\n    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 24 -noSplitSubreads<\/blasr>\r\n    <input baseDir=\"\u8f93\u5165Pacbio\u6570\u636e\u6587\u4ef6\u6240\u5728\u7684\u6587\u4ef6\u5939\">\r\n        <job>Pacbio\u6570\u636e\u6587\u4ef6\u540d\u79f0<\/job>\r\n    <\/input>\r\n<\/jellyProtocol>\r\n<\/pre>\n
\u7136\u540e\u4f9d\u6b21\u8fd0\u884c\u4e0b6\u6b65\uff1a<\/p>\n
\r\n$ Jelly.py setup Protocol.xml\r\n$ Jelly.py mapping Protocol.xml\r\n$ Jelly.py support Protocol.xml\r\n$ Jelly.py extraction Protocol.xml\r\n$ Jelly.py assembly Protocol.xml -x \"--nproc=24\"\r\n$ Jelly.py output Protocol.xml\r\n\r\n--nproc \u53c2\u6570\u8bbe\u7f6e\u8fd0\u884c\u7ebf\u7a0b\u6570\u3002\r\n<\/pre>\n
\u8f93\u51fa\u7ed3\u679c\u6587\u4ef6\u4e3a jelly.out.fasta \u3002<\/p>\n
4. \u4f7f\u7528 PBJelly2 \u8fdb\u884c scaffold \u8fde\u63a5<\/h1>\n","protected":false},"excerpt":{"rendered":"
1.PBJelly2 \u7b80\u4ecb PBJelly2 \u7528\u4e8e\u5229\u7528 Pacbio \u6570\u636e\u8fdb\u884c\u57fa … \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":[66],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2270"}],"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=2270"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2270\/revisions"}],"predecessor-version":[{"id":2272,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2270\/revisions\/2272"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2270"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2270"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2270"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}