{"id":2276,"date":"2015-08-25T16:29:43","date_gmt":"2015-08-25T08:29:43","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2276"},"modified":"2015-08-25T16:29:43","modified_gmt":"2015-08-25T08:29:43","slug":"%e4%bd%bf%e7%94%a8-sga-%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=2276","title":{"rendered":"\u4f7f\u7528 SGA \u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"<h1>1. SGA \u7b80\u4ecb<\/h1>\n<p><a href=\"https:\/\/github.com\/jts\/sga\" target=\"_blank\">SGA<\/a> (String Graph Assembler), \u91c7\u7528 String Grapher \u7684\u65b9\u6cd5\u6765\u8fdb\u884c\u57fa\u56e0\u7ec4\u7684\u7ec4\u88c5\u3002\u8f6f\u4ef6\u901a\u8fc7\u521b\u5efa FM-index\/Burrows-Wheeler \u7d22\u5f15\u6765\u8fdb\u884c\u67e5\u627e short reads \u4e4b\u95f4\u7684 overlaps\uff0c \u4ece\u800c\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5\u3002<br \/>\n\u4f7f\u7528 SGA \u7684\u6ce8\u610f\u4e8b\u9879\uff1a<\/p>\n<pre>\r\n1. SGA \u7684\u8f93\u5165\u6587\u4ef6\u4e3a fastq \u6587\u4ef6\uff0c\u5e8f\u5217\u957f\u5ea6\u63a8\u8350\u4e3a 100bp \u53ca\u4ee5\u4e0a\u3002\u8f83\u77ed\u7684\u5e8f\u5217\u957f\u5ea6\uff0c\u5219\u4f7f\u7528 De Bruijn \u7684\u65b9\u6cd5\u8fdb\u884c\u7ec4\u88c5\u80fd\u6216\u5f97\u66f4\u597d\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002\r\n2. \u4f7f\u7528 SGA \u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5\u9700\u8981\u6700\u5c11 40X\r\n<\/pre>\n<h1>2. SGA \u5b89\u88c5<\/h1>\n<p>SGA \u7684\u5b89\u88c5\u4e0e\u4f7f\u7528\u9700\u8981\u4f9d\u8d56 <a href=\"http:\/\/code.google.com\/p\/google-sparsehash\/\" target=\"_blank\">google-sparsehash<\/a>, <a href=\"https:\/\/github.com\/pezmaster31\/bamtools\" target=\"_blank\">bamtools<\/a>, zlib \u548c <a href=\"http:\/\/www.canonware.com\/jemalloc\/download.html\" target=\"_blank\">jemalloc<\/a> \u7b49\u8f6f\u4ef6\u3002<\/p>\n<pre>\r\n\u5b89\u88c5 goolge-sparsehash\uff0c\u7531\u4e8e\u56fd\u5185\u5c4f\u853d\u4e86google\uff0c\u65e0\u6cd5\u4e0b\u8f7d\u8be5\u8f6f\u4ef6\u3002\r\n$ wget www.chenlianfu.com\/public\/software\/sparsehash-2.0.2.tar.gz\r\n$ tar zxf sparsehash-2.0.2.tar.gz\r\n$ cd sparsehash-2.0.2\r\n$ .\/configure && make -j 8 && sudo make install\r\n\r\n\u5b89\u88c5 bamtools\r\n$ wget https:\/\/github.com\/pezmaster31\/bamtools\/archive\/master.zip -O bamtools.zip\r\n$ unzip bamtools.zip\r\n$ cd bamtools-master\/\r\n$ mkdir build; cd build\r\n$ cmake ..\/\r\n$ make -j 8\r\n$ cd ..\/..\/\r\n$ mv bamtools-master\/ \/opt\/biosoft\/bamtools\r\n\r\n\u5b89\u88c5 jemalloc\uff0c\u53ef\u9009\uff0c\u6709\u5229\u4e8e\u51cf\u5c11\u8fd0\u7b97\u65f6\u95f4\u3002\r\n$ wget https:\/\/github.com\/jemalloc\/jemalloc\/archive\/dev.zip -O jemalloc.zip\r\n$ unzip jemalloc.zip\r\n$ .\/autogen.sh \r\n$ .\/configure && make -j 8 && sudo make install\r\n$ cd ..\/\r\n$ mkdir \/opt\/biosoft\/sga\/\r\n$ mv jemalloc-dev \/opt\/biosoft\/sga\/\r\n\r\n\u5b89\u88c5 SGA\r\n$ wget https:\/\/github.com\/jts\/sga\/archive\/master.zip -O sga.zip\r\n$ unzip sga.zip\r\n$ cd sga-master\/src\r\n$ .\/autogen.sh\r\n$ .\/configure --with-bamtools=\/opt\/biosoft\/bamtools --with-jemalloc=\/opt\/biosoft\/sga\/jemalloc-dev\/lib\/ --prefix=\/opt\/biosoft\/sga\/\r\n$ make -j 8\r\n$ make install\r\n$ cd ..\r\n$ mv * \/opt\/biosoft\/sga\/\r\n$ echo 'PATH=\/opt\/biosoft\/sga\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n\r\n\u6b64\u5916\uff0c\u5982\u679c\u9700\u8981\u4f7f\u7528\u7a0b\u5e8f\u9644\u5e26\u7684\u4e00\u4e9b python \u7a0b\u5e8f\uff0c\u5219\u9700\u8981\u5b89\u88c5\u4e00\u4e9b python \u6a21\u5757\u3002\r\n$ wget https:\/\/pypi.python.org\/packages\/source\/r\/ruffus\/ruffus-2.6.3.tar.gz\r\n$ tar zxf ruffus-2.6.3.tar.gz\r\n$ cd ruffus-2.6.3\r\n$ sudo python setup.py install\r\n\r\n<\/pre>\n<h1>3. SGA \u7684\u4f7f\u7528<\/h1>\n<p>SGA \u5305\u542b\u5f88\u591a\u4e2a\u547d\u4ee4\uff0c\u76f4\u63a5\u8f93\u5165\u547d\u4ee4\uff0c\u5373\u53ef\u5f97\u5230\u5e2e\u52a9\u4fe1\u606f\u3002<br \/>\n\u4ee5 2 \u4e2a PE \u6587\u5e93\u548c 2 \u4e2a MP \u6587\u5e93\u7684\u6d4b\u5e8f\u6570\u636e\u4e3a\u8f93\u5165\uff0c\u4f7f\u7528 SGA \u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u6765\u4ecb\u7ecd\u8fd0\u884c\u6d41\u7a0b\u3002<br \/>\n\u8f93\u5165\u6587\u4ef6\uff1a<\/p>\n<pre>\r\npe180.1.fastq    pe180.2.fastq\r\npe500.1.fastq    pe500.2.fastq\r\nmp2000.1.fastq   mp2000.2.fastq\r\nmp5000.1.fastq   mp5000.2.fastq\r\n<\/pre>\n<h2>3.1 \u6570\u636e\u9884\u5904\u7406<\/h2>\n<p>\u4f7f\u7528 preprocess \u7a0b\u5e8f\u8fdb\u884c\u4f4e\u8d28\u91cf\u6570\u636e\u7684\u622a\u77ed\u548c\u5220\u9664,\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n\u53bb\u9664 PE \u6587\u5e93\u6570\u636e\u4e2d\u542b\u6709 N \u7684reads\u3002\u6b64\u5904\u4ec5\u5bf9\u9700\u8981\u8fdb\u884c contig \u7ec4\u88c5\u7684 PE \u6570\u636e\u8fdb\u884c\u5904\u7406\u3002\r\n$ sga preprocess -o pe180.pp.fastq --pe-mode 1 pe180.1.fastq pe180.2.fastq\r\n$ sga preprocess -o pe500.pp.fastq --pe-mode 1 pe500.1.fastq pe500.2.fastq\r\n\r\n\u7ed3\u679c\u4e2d pp \u8868\u793a preprocess \u7684\u610f\u601d\u3002\r\n\u4e00\u822c\u7528\u5176\u5b83\u8f6f\u4ef6\u8fdb\u884c Fastq \u6587\u4ef6\u7684 QC\uff0c\u6b64\u5904\u4f7f\u7528 preprocess \u53bb\u9664\u542b\u6709 N \u7684 reads \u5373\u53ef\u3002\u7531\u4e8e\u8f6f\u4ef6\u540e\u7eed\u6709\u5bf9 reads \u7684\u6821\u6b63\u8fc7\u7a0b\uff0c\u56e0\u6b64\u4e0d\u63a8\u8350\u5bf9 reads \u8fdb\u884c\u622a\u77ed\u5904\u7406\u3002\r\n<\/pre>\n<p>preprocess \u547d\u4ee4\u53c2\u6570\uff1a<\/p>\n<pre>\r\nsga preprocess [OPTION] READS1 READS2 ...\r\n\r\n-o | --output FILE\r\n    \u5c06\u8f93\u51fa\u6570\u636e\u5199\u5165\u5230\u8be5\u6587\u4ef6\u4e2d\u3002\u9ed8\u8ba4\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\u3002\u7a0b\u5e8f\u4ec5\u5f97\u5230\u4e00\u4e2a\u8f93\u51fa\u6587\u4ef6\u3002\u6210\u5bf9\u7684\u6570\u636e\u7528 \/1 \/2 \u6807\u8bc6\u51fa\u6765\u5e76\u5728\u8f93\u51fa\u6587\u4ef6\u4e2d\u4ea4\u53c9\u6392\u5217\u3002\r\n-p | --pe-mode INT\r\n    paired end \u6a21\u5f0f\u3002 \u6709 3 \u4e2d\u6a21\u5f0f\uff0c\u7528\u6570\u5b57 0, 1, 2 \u8868\u793a\u3002\r\n    0\uff1a\u8868\u793a\u8ba4\u4e3a\u8f93\u5165\u6570\u636e\u90fd\u662f\u5355\u7aef\u6570\u636e\uff1b\r\n    1\uff1a\u8868\u793a READS1 \u4e2d\u7684\u6570\u636e\u548c READS2 \u4e2d\u7684\u6570\u636e\u662f\u6210\u5bf9\u7684\uff0c\u8fd9\u79cd\u60c5\u51b5\u4e0b\u82e5\u6709\u4e00\u6761 read \u88ab\u53bb\u9664\uff0c\u5219\u5bf9\u5e94\u7684\u53e6\u5916\u4e00\u6761\u4e5f\u4f1a\u88ab\u53bb\u9664\uff1b\r\n    2\uff1a\u8868\u793a reads \u662f\u6210\u5bf9\u7684\uff0c\u53ef\u80fd\u8be5\u503c\u9002\u5408\u4e8e3\u4e2a\u53ca\u4ee5\u4e0a\u6587\u4ef6\u4f5c\u4e3a\u8f93\u5165\uff08\u6211\u6ca1\u6709\u7528\u8fc7\uff09\u3002\r\n--pe-orphans FILE\r\n    \u5982\u679c read pair \u4e2d\u6709\u4e00\u6761\u5e8f\u5217\u88ab\u53bb\u9664\uff0c\u5219\u53e6\u5916\u4e00\u6761\u5e8f\u5217\u5199\u5165\u5230\u6b64\u6587\u4ef6\u4e2d\u3002\r\n--phred64\r\n    \u52a0\u5165\u8be5\u53c2\u6570\uff0c\u8868\u660e\u8f93\u5165\u7684 fastq \u6587\u4ef6\u4e3a phred64 \u683c\u5f0f\uff0c\u8f93\u51fa\u7ed3\u679c\u4f1a\u8f6c\u6362\u6210 phred33 \u683c\u5f0f\u3002\r\n--discard-quality\r\n    \u4e0d\u8f93\u51fa\u78b1\u57fa\u8d28\u91cf\u3002\r\n-q | --quality-trim INT\r\n    \u5bf9\u4f4e\u8d28\u91cf\u78b1\u57fa\u8fdb\u884c trim\u3002\r\n-f | --quality-filter INT\r\n    \u5bf9\u4f4e\u8d28\u91cf reads \u8fdb\u884c\u53bb\u9664\u3002\u82e5 read \u4e2d\u78b1\u57fa\u8d28\u91cf <=3 \u7684\u4f4e\u8d28\u91cf\u78b1\u57fa\u591a\u4f59\u8be5\u503c\uff0c\u5219\u53bb\u9664\u6574\u6761 read\u3002\r\n-m | --min-length INT\r\n    \u53bb\u9664\u957f\u5ea6\u4f4e\u4e8e\u6b64\u503c\u7684 read\u3002\r\n-h | --hard-clip INT\r\n    \u5c06\u6240\u6709\u7684 reads \u957f\u5ea6\u622a\u77ed\u5230\u8be5\u503c\u3002\r\n--permute-ambiguous\r\n    \u5c06 reads \u4e2d\u7684 N \u968f\u673a\u66ff\u6362\u4e3a ATCG \u4e2d\u7684\u4e00\u79cd\u3002\r\n--dust\r\n    \u53bb\u9664\u4f4e\u590d\u6742\u5ea6 reads \u3002\r\n-dust-threshold FLOAT\r\n    \u53bb\u9664 dust score \u9ad8\u4e8e\u6b64\u503c\u7684 reads\u3002\u9ed8\u8ba4\u4e3a 4.0 \u3002\r\n--suffix STRING\r\n    \u5728\u6bcf\u4e2a read ID \u540e\u6dfb\u52a0\u540e\u7f00\u3002\r\n--no-primer-check\r\n    \u4e0d\u8fdb\u884c primer \u5e8f\u5217\u68c0\u6d4b\r\n-r | --remove-adapter-fwd  STRING\r\n    \u53bb\u9664 adapter \u5e8f\u5217\uff0c\u63d0\u4f9b adapter \u5e8f\u5217\u7684\u7b2c\u4e00\u6761\u94fe\u3002\r\n-c | --remove-adapter-rev STRING\r\n    \u53bb\u9664 adapter \u5e8f\u5217\uff0c\u63d0\u4f9b adapter \u5e8f\u5217\u7684\u7b2c\u4e8c\u6761\u94fe\u3002\r\n<\/pre>\n<h2>2. FM \u7d22\u5f15\u6784\u5efa\u4e0e\u5408\u5e76<\/h2>\n<p>\u4f7f\u7528 index \u547d\u4ee4\u5bf9 reads \u6570\u636e\u6784\u5efa\u7d22\u5f15\u3002\u5f53\u4f7f\u7528\u591a\u7ec4\u6570\u636e\u8fdb\u884c contig \u7ec4\u88c5\u7684\u65f6\u5019\uff0c\u4f7f\u7528 merge \u5bf9\u591a\u7ec4\u6570\u636e\u7684\u7d22\u5f15\u8fdb\u884c\u5408\u5e76\u3002\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n$ sga index -a ropebwt -t 8 --no-reverse pe180.pp.fastq\r\n$ sga index -a ropebwt -t 8 --no-reverse pe500.pp.fastq\r\n\r\n$ sga merge -t 8 -p pe -r pe180.pp.fastq pe500.pp.fastq\r\n<\/pre>\n<p>index \u547d\u4ee4\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\nsga index [OPTION] ... READSFILE\r\n\r\n-a | --algorithm STRING\r\n    BWT \u6784\u5efa\u7b97\u6cd5\uff0c\u6709\u4e24\u79cd sais \uff08\u9ed8\u8ba4\uff09 \u548c ropebwt\u3002\u524d\u8005\u9002\u5408\u4e0e\u8f83\u957f\u7684 reads\uff1b\u540e\u8005\u9002\u5408\u4e0e\u8f83\u77ed\u7684\uff08<200bp\uff09 reads,\u4f46\u662f\u901f\u5ea6\u5feb\uff0c\u6d88\u8017\u5185\u5b58\u5c11\u3002\r\n-t | --threads INT\r\n    \u8fd0\u7b97\u7684\u7ebf\u7a0b\u6570\u3002\u9ed8\u8ba4\u4e3a 1 \u3002\r\n-p | --prefix\r\n    \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u524d\u7f00\uff0c\u9ed8\u8ba4\u4e3a\u8f93\u5165\u6587\u4ef6\u7684\u524d\u7f00\u3002\r\n--no-reverse\r\n    \u4e0d\u751f\u6210\u53cd\u5411\u5e8f\u5217\u7684 BWT \u6587\u4ef6\u3002\u7531\u4e8e\u5bf9\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u6821\u6b63\u7684\u65f6\u5019\u4e0d\u8bb8\u8981\u8be5\u6587\u4ef6\uff0c\u4e00\u822c\u52a0\u5165\u8be5\u53c2\u6570\u4ee5\u8282\u7ea6\u8d44\u6e90\u3002\r\n--no-forward\r\n    \u4e0d\u751f\u6210\u6b63\u5411\u5e8f\u5217\u7684 BWT \u6587\u4ef6\u3002\r\n--no-sai\r\n    \u4e0d\u751f\u6210 SAI \u6587\u4ef6\u3002\r\n<\/pre>\n<p>merge \u547d\u4ee4\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\nsga merge [OPTION] ... READS1 READS2\r\n\r\n-t | --threads INT\r\n    \u8fd0\u7b97\u7684\u7ebf\u7a0b\u6570\u3002\u9ed8\u8ba4\u4e3a 1 \u3002\r\n-p | --prefix \r\n    \u6307\u5b9a\u8f93\u51fa\u6587\u4ef6\u524d\u7f00\uff0c\u9ed8\u8ba4\u4e3a\u8f93\u5165\u6587\u4ef6\u7684\u524d\u7f00\u3002\r\n-r | --remove\r\n    \u751f\u6210\u5408\u5e76\u540e\u7684 index \u6587\u4ef6\u540e\uff0c\u5220\u9664\u65e7\u7684 index \u6587\u4ef6\u548c fastq \u6587\u4ef6\u3002\r\n<\/pre>\n<h2>3. reads \u7684\u6821\u6b63<\/h2>\n<p>\u4f7f\u7528 correct \u547d\u4ee4\u5bf9 reads \u8fdb\u884c\u6821\u6b63\uff0c\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n$ sga correct -t 8 -k 41 -x 2 --learn -o pe.ec.fastq pe.fastq\r\n<\/pre>\n<p>correct \u547d\u4ee4\u53c2\u6570\uff1a<\/p>\n<pre>\r\nsga correct [OPTION] ... READSFILE\r\n\r\n-p | --prefix STRING\r\n    \u8f93\u5165\u7684 index \u6587\u4ef6\u7684\u524d\u7f00\uff0c\u9ed8\u8ba4\u4e3a\u8f93\u5165\u6587\u4ef6\u7684\u524d\u7f00\u3002\r\n-o | --outfile STRING\r\n    \u5c06\u6821\u6b63\u540e\u7684\u6570\u636e\u5199\u5165\u5230\u6b64\u6587\u4ef6\u4e2d\uff0c\u9ed8\u8ba4\u8f93\u51fa\u7684\u6587\u4ef6\u540d\u4e3a READSFILE.ec.fa\u3002\u867d\u7136\u540e\u7f00\u662f fa\uff0c\u4f46\u5176\u5b9e\u662f fastq \u6587\u4ef6\u3002\r\n-t | --threads INT\r\n    \u8fd0\u7b97\u7684\u7ebf\u7a0b\u6570\u3002\u9ed8\u8ba4\u4e3a 1 \u3002\r\n--discard\r\n    \u68c0\u6d4b\u5e76\u53bb\u9664\u4f4e\u8d28\u91cf reads \u3002\r\n-a | --algorithm STRING\r\n    \u8fdb\u884c reads correction \u7684\u7b97\u6cd5\u3002\u6709 3 \u79cd\uff1a\r\n    kmer\uff1a \u4f7f\u7528 kmer \u7684\u65b9\u6cd5\u8fdb\u884c\u6821\u6b63\uff0c\u9ed8\u8ba4\u662f\u8be5\u503c\uff1b\r\n    overlap\uff1a\u57fa\u4e8e\u91cd\u53e0\u7684\u65b9\u6cd5\u8fdb\u884c\u6821\u6b63\uff1b\r\n    hybrid\uff1a\u5e94\u8be5\u662f\u540c\u65f6\u4e0a\u9762 2 \u4e2d\u65b9\u6cd5\u8fdb\u884c\u6821\u6b63\u3002\r\n--metrics FILE\r\n    \u6821\u6b63\u540e\uff0c\u5c06 read \u4e2d\u6bcf\u4e2a\u4f4d\u70b9\u7684\u78b1\u57fa\u9519\u8bef\u7387\u5199\u5165\u5230\u8be5\u6587\u4ef6\u3002\r\n\r\n\u4f7f\u7528 kmer \u65b9\u6cd5\u8fdb\u884c\u6821\u6b63\u7684\u53c2\u6570\uff1a\r\n-k | --kerm-size INT\r\n    \u9009\u53d6\u7684 kemr \u957f\u5ea6\uff0c\u9ed8\u8ba4\u4e3a 31 \u3002\r\n-x | --kmer-threshold INT\r\n    \u5bf9\u51fa\u73b0\u6b21\u6570\u4f4e\u4e8e\u6b64\u503c\u7684 kmer \u8fdb\u884c\u6821\u6b63\u3002\u9ed8\u8ba4\u4e3a 3 \u3002\r\n-i | --kmer-rounds INT\r\n    \u6267\u884c N \u8f6e\u6821\u6b63\uff0c\u6700\u591a\u6821\u6b63 N \u4e2a\u78b1\u57fa\u3002\u9ed8\u8ba4\u7684 N \u503c\u4e3a 10\u3002\r\n--learn\r\n    \u7a0b\u5e8f\u81ea\u884c\u8ba1\u7b97 -x \u7684\u53c2\u6570\u3002\u82e5\u6d4b\u5e8f\u8986\u76d6\u5ea6\u4f4e\u4e8e 20x \u6216\u6d4b\u5e8f\u6570\u636e\u5728\u57fa\u56e0\u7ec4\u4e0a\u7684\u8986\u76d6\u4e0d\u5747\u5300\uff0c\u5219\u4e0d\u9002\u5408\u9009\u62e9\u8be5\u53c2\u6570\u3002\r\n\r\n\u4f7f\u7528 overlap \u65b9\u6cd5\u8fdb\u884c\u6821\u6b63\u7684\u53c2\u6570\uff1a\r\n-e | --error-rate    default:0.04\r\n    2 \u6761 reads \u6709 overlap \u65f6\uff0c\u5141\u8bb8\u7684\u6700\u5927\u9519\u8bef\u7387\u3002\r\n-m | --min-overlap    default:45\r\n    2 \u6761 reads \u91cd\u53e0\u7684\u6700\u5c0f\u78b1\u57fa\u6570\u3002\r\n-c | --conflict    default:5\r\n    \u68c0\u6d4b\u51fa\u4e00\u4e2a\u9519\u8bef\u78b1\u57fa\u6240\u9700\u8981\u7684\u6700\u5c0f\u91cd\u53e0\u6570\u76ee\u3002\r\n-r | --rounds    default:1\r\n    \u8fdb\u884c\u8fed\u4ee3\u6821\u6b63\u7684\u6307\u5b9a\u7684\u6b21\u6570\u3002\r\n<\/pre>\n<h2>4. reads \u7684\u8fc7\u6ee4<\/h2>\n<p>\u53bb\u9664\u6570\u636e\u4e2d\u5b8c\u5168\u4e00\u6a21\u4e00\u6837\u7684 duplicate\uff1b\u53bb\u9664\u542b\u6709\u4f4e\u9891 kmer \u7684 reads\u3002\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n\u9700\u8981\u5148\u5bf9\u6821\u6b63\u8fc7\u540e\u7684\u6570\u636e\u91cd\u65b0\u6784\u5efa index\r\n$ sga index -a ropebwt -t 8 pe.ec.fastq\r\n\r\n$ sga filter -x 2 -t 8 -o pe.ec.f.fastq --homopolymer-check --low-complexity-check pe.ec.fastq\r\n<\/pre>\n<p>filter \u547d\u4ee4\u5e38\u7528\u53c2\u6570:<\/p>\n<pre>\r\nsga filter [OPTION] ... READSFILE\r\n\r\n-o | --outfile STRING\r\n    \u5c06\u6821\u6b63\u540e\u7684\u6570\u636e\u5199\u5165\u5230\u6b64\u6587\u4ef6\u4e2d\uff0c\u9ed8\u8ba4\u8f93\u51fa\u7684\u6587\u4ef6\u540d\u4e3a READSFILE.filter.pass.fa \u3002\r\n--no-duplicate-check\r\n    \u4e0d\u8fdb\u884c duplicate removal\r\n--no-kmer-check\r\n    \u4e0d\u8fdb\u884c kmer check\r\n--kmer-both-strand\r\n    \u5bf9 reads \u7684\u6b63\u8d1f\u94fe\u90fd\u8fdb\u884c\u68c0\u6d4b\r\n--homopolymer-check\r\n    \u68c0\u6d4b\u5355\u78b1\u57fa\u8fde\u7eed\u60c5\u51b5\r\n--low-complexity-check\r\n    \u53bb\u9664\u4f4e\u91cd\u590d reads\r\n-k | --kmer-size    default:27\r\n    kmer \u68c0\u6d4b\u65f6\u6240\u7528\u7684 kmer \u503c\u3002\r\n-x | --kmer-threshold     default:3\r\n    \u4fdd\u7559\u7684 read \u4e2d\u6240\u6709\u7684 kemr \u7684\u8986\u76d6\u5ea6\u5fc5\u987b\u5927\u4e8e\u8be5\u503c\u3002\r\n<\/pre>\n<h2>5. \u6574\u5408\u51fa\u7b80\u5355\u7684\u5e8f\u5217<\/h2>\n<p>\u4f7f\u7528 fm-merge \u6574\u5408\u51fa\u4e00\u4e9b\u7b80\u5355\u5e8f\u5217\uff08simple unbranched chains\uff09\uff0c\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n$ sga fm-merge -m 55 -t 8 -o merged.fa pe.ec.f.fastq\r\n<\/pre>\n<p>fm-merge \u547d\u4ee4\u53c2\u6570\uff1a<\/p>\n<pre>\r\nsga fm-merge [OPTION] ... READSFILE\r\n\r\n-m | --min-overlap    default:45\r\n    2 \u4e2a reads \u4e4b\u95f4\u6700\u5c0f\u7684 ovlerlap \u957f\u5ea6\u3002\u6b64\u503c\u8bbe\u7f6e\u8fc7\u5c0f\uff0c\u5219\u6d88\u8017\u66f4\u591a\u7684\u8ba1\u7b97\u65f6\u95f4\u3002\r\n<\/pre>\n<h2>6. \u53bb\u9664\u91cd\u590d\u5e8f\u5217<\/h2>\n<p>\u5728\u4e0a\u4e00\u6b65\u547d\u4ee4\u4e4b\u540e\uff0c\u751f\u6210\u7684\u5e8f\u5217\u4e2d\uff0c\u6709\u5f88\u591a\u7684\u5305\u542b\u4e0e\u88ab\u5305\u542b\u7684\u5173\u7cfb\uff0c\u4f7f\u7528 rmdup \u547d\u4ee4\u53bb\u9664 substrings \u5e8f\u5217\u3002\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n$ sga index -d 1000000 merged.fa\r\n$ sga rmdup -t 8 -o rmdup.fa merged.fa\r\n<\/pre>\n<p>rmdup \u547d\u4ee4\u53c2\u6570\uff1a<\/p>\n<pre>\r\nsga rmdup [OPTION] ... READFILE\r\n\r\n-o | --out FILE    default:READFILE.rmdup.fa\r\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u540d\u3002\r\n-e | --error-rate    default: exact matches required\r\n    \u8bbe\u5b9a 2 \u6761\u5e8f\u5217\u4e00\u81f4\uff0c\u8fd9 2 \u6761\u4e4b\u95f4\u7684\u5141\u8bb8\u7684\u6700\u5927\u9519\u8bef\u7387\u3002\u9ed8\u8ba4 2 \u6761\u5e8f\u5217\u5fc5\u987b\u5b8c\u5168\u4e00\u81f4\u3002\r\n<\/pre>\n<h2>7. \u6784\u5efa string grahp<\/h2>\n<p>\u4f7f\u7528 overlap \u547d\u4ee4\u6765\u6784\u5efa string graph\u3002\u5982\u679c\u7ec4\u88c5\u5c0f\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\uff0c\u53ef\u4ee5\u8df3\u8fc7 fm-merge \u548c rmdup \u8fd9 2 \u6b65\u3002\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n$ sga overlap -m 55 -t 8 rmdup.fa\r\n<\/pre>\n<p>overlap \u547d\u4ee4\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-m | --min-overlap    default:45\r\n    2 \u4e2a reads \u4e4b\u95f4\u6700\u5c0f\u7684 ovlerlap \u957f\u5ea6\u3002\u6b64\u503c\u8bbe\u7f6e\u8fc7\u5c0f\uff0c\u5219\u6d88\u8017\u66f4\u591a\u7684\u8ba1\u7b97\u65f6\u95f4\u3002\r\n<\/pre>\n<h2>7. \u7ec4\u88c5 contigs<\/h2>\n<p>\u4f7f\u7528\u547d\u4ee4 assemble \u8fdb\u884c contigs \u7ec4\u88c5\uff0c\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n$ sga assemble -m 75 -g 0 -r 10 -o assemble.m75 rmdup.asqg.gz\r\n<\/pre>\n<p>assemble \u547d\u4ee4\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-m | --min-overlap    default:45\r\n    2 \u4e2a reads \u4e4b\u95f4\u6700\u5c0f\u7684 ovlerlap \u957f\u5ea6\u3002\u5f53\u53c2\u6570\u5728 fm-merge, overlap \u548c assemble \u8fd9 3 \u4e2a\u547d\u4ee4\u4e2d\u90fd\u6709\u51fa\u73b0\u3002\u5f53\u6d4b\u5e8f reads \u957f\u5ea6\u4e3a 100bp \u65f6\uff0c \u8be5\u53c2\u6570\u7684\u503c\u5728 3 \u4e2a\u547d\u4ee4\u4e2d\u6bd4\u8f83\u5408\u9002\u7684\u503c\u5206\u522b\u662f 65, 65, 75\u3002\u5f53\u7136\uff0c reads \u957f\u5ea6\u8d8a\u957f\uff0c\u5219\u8be5\u53c2\u6570\u7684\u503c\u8bbe\u7f6e\u8d8a\u5927\u3002\u6b64\u5916\uff0c\u4e00\u822c\u901a\u8fc7\u8c03\u8282 overlap \u4e2d\u8be5\u53c2\u6570\u7684\u503c\u6765\u4f18\u5316\u7ec4\u88c5\u7ed3\u679c\u3002\r\n-d | --max-divergence    default:0.05\r\n    \u5982\u679c\u5e8f\u5217\u4e2d\u7684 SNP \u6bd4\u7387 < 0.05\uff0c\u5219\u6d88\u9664\u53d8\u5f02\u3002\u5f53\u57fa\u56e0\u7ec4\u6742\u5408\u7387\u975e\u5e38\u9ad8\u65f6\uff0c\u9700\u8981\u589e\u5927\u8be5\u503c\u3002\r\n-g | --max-gap-divergence    default:0.01\r\n    \u5982\u679c\u5e8f\u5217\u4e2d\u7684 INDEL \u6bd4\u7387 < 0.01\uff0c\u5219\u6d88\u9664\u53d8\u5f02\u3002\u5f53\u57fa\u56e0\u7ec4\u6742\u5408\u7387\u975e\u5e38\u9ad8\u65f6\uff0c\u9700\u8981\u589e\u5927\u8be5\u503c\u3002\u5982\u679c\u8bbe\u7f6e\u6539\u503c\u4e3a 0\uff0c \u5219\u8868\u793a\u4e0d\u6d88\u9664\u53d8\u5f02\u3002\r\n--max-indel    default\uff1a20\r\n    \u5f53 indel \u957f\u5ea6\u5927\u4e8e\u8be5\u503c\u7684\u65f6\u5019\uff0c\u5219\u4e0d\u6d88\u9664\u53d8\u5f02\u3002\r\n-l | --min-branch-length    default:150\r\n    \u53bb\u9664 tip \u5e8f\u5217\uff0c\u5982\u679c\u5176\u5e8f\u5217\u957f\u5ea6\u4f4e\u4e8e\u8be5\u503c\u3002\u5f53 reads \u957f\u5ea6\u4e3a 100 bp \u65f6\u5019\uff0c\u63a8\u8350\u8bbe\u7f6e\u4e3a 150\uff1b\u82e5 reads \u957f\u5ea6\u8d8a\u5927\uff0c\u8be5\u503c\u4e5f\u9700\u8981\u8d8a\u5927\u3002\r\n-r | --resolve-small    default: not perfomed\r\n    \u5bf9 samll repeat \u5e8f\u5217\u8fdb\u884c\u6253\u65ad\uff0c\u5982\u679c\u8be5\u8de8\u8fc7\u8be5\u533a\u57df\u7684 overlaps \u4e4b\u95f4\u7684\u6700\u5927\u957f\u5ea6\u5dee\u8d85\u8fc7\u8be5\u503c\u65f6\u3002\u53ef\u4ee5\u8bbe\u7f6e\u8be5\u503c\u4e3a 10 \u3002\r\n<\/pre>\n<h2>7. \u7ec4\u88c5 scaffold<\/h2>\n<p>\u9996\u5148\uff0c\u9700\u8981\u5c06 PE \u548c MP \u6570\u636e\u6bd4\u5bf9\u5230 contigs \u5e8f\u5217\u4e0a<\/p>\n<pre>\r\n$ \/opt\/biosoft\/sga\/src\/bin\/sga-align --name pe180 assemble.m75-contigs.fa pe180.1.fastq pe180.2.fastq\r\n$ \/opt\/biosoft\/sga\/src\/bin\/sga-align --name pe250 assemble.m75-contigs.fa pe250.1.fastq pe250.2.fastq\r\n$ \/opt\/biosoft\/sga\/src\/bin\/sga-align --name mp2000 assemble.m75-contigs.fa mp2000.1.fastq mp2000.2.fastq\r\n$ \/opt\/biosoft\/sga\/src\/bin\/sga-align --name mp5000 assemble.m75-contigs.fa mp5000.1.fastq mp5000.2.fastq\r\n<\/pre>\n<p>\u7136\u540e\uff0c\u8ba1\u7b97 contig \u4e4b\u95f4\u7684\u8ddd\u79bb<\/p>\n<pre>\r\n$ sga-bam2de.pl -n 5 --prefix pe180 pe180.bam\r\n$ sga-bam2de.pl -n 5 --prefix pe500 pe500.bam\r\n$ sga-bam2de.pl -n 5 --prefix mp2000 mp2000.bam\r\n$ sga-bam2de.pl -n 5 --prefix mp5000 mp5000.bam\r\n<\/pre>\n<p>\u518d\u8ba1\u7b97 contig \u7684\u62f7\u8d1d\u6570<\/p>\n<pre>\r\n$ sga-astat.py -m 200 pe180.refsort.bam > pe180.astat\r\n$ sga-astat.py -m 200 pe500.refsort.bam > pe500.astat\r\n<\/pre>\n<p>\u6700\u540e\uff0c\u8fdb\u884c scaffold \u7ec4\u88c5<\/p>\n<pre>\r\n$ sga scaffold -m 200 -a pe180.astat -a pe500.astat -pe pe180.de --pe pe500.de --mp mp2000.de --mp mp5000.de -o genome.scaf assemble.m75-contigs.fa\r\n$ sga scaffold2fasta -m 200 -a assemble.m75-graph.asqg.gz -o genomeScaffold.n5.fa -d 1 --use-overlap --write-unplaced genome.scaf\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. SGA \u7b80\u4ecb SGA (String Graph Assembler),  &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2276\">\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":[3],"tags":[39],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2276"}],"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=2276"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2276\/revisions"}],"predecessor-version":[{"id":2277,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2276\/revisions\/2277"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2276"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2276"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2276"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}