{"id":1914,"date":"2013-10-11T10:03:34","date_gmt":"2013-10-11T02:03:34","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1914"},"modified":"2013-10-15T20:21:15","modified_gmt":"2013-10-15T12:21:15","slug":"ebardenovo-a-rna-seq-assembler","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1914","title":{"rendered":"EBARDenovo : A RNA-Seq Assembler"},"content":{"rendered":"

1. How to Install EBARDenovo on Linux<\/h1>\n

mono is demanded for runing EBARDenovo on linux.<\/p>\n

yum install gcc gcc-c++ bison pkgconfig glib2-devel gettext make libpng-devel libjpeg-devel libtiff-devel libexif-devel giflib-devel libX11-devel freetype-devel fontconfig-devel  cairo-devel httpd httpd-devel\r\n\r\n$ wget http:\/\/download.mono-project.com\/sources\/libgdiplus\/libgdiplus-2.10.tar.bz2\r\n$ tar jxf libgdiplus-2.10.tar.bz2\r\n$ .\/configure --prefix=\/opt\/mono\r\n$ make -j 8; make install\r\n$ echo 'export LD_LIBRARY_PATH=\/opt\/mono\/lib:$LD_LIBRARY_PATH' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n\r\n$ wget http:\/\/download.mono-project.com\/sources\/mono\/mono-2.10.8.tar.bz2\r\n$ tar jxf mono-2.10.8.tar.bz2\r\n$ cd mono-2.10.8\r\n$ .\/configure --prefix=\/opt\/mono\r\n$ make -j 8\r\n$ make install\r\n$ echo 'export PKG_CONFIG_PATH=\/opt\/mono\/lib\/pkgconfig:$PKG_CONFIG_PATH' >> ~\/.bashrc\r\n$ echo 'export PATH=\/opt\/mono\/bin:$PATH' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n\r\n$ wget http:\/\/ncu.dl.sourceforge.net\/project\/ebardenovo\/EBARDenovo-1.2.2-20130404.zip\r\n$ unzip EBARDenovo-1.2.2-20130404.zip\r\n$ cd EBARDenovo-1.2.2-20130404\/\r\n$ mono EBARDenovo.exe -h<\/pre>\n
2. The parameters<\/h1>\n
Display parameters\r\n-l :  no log file\r\n-v :  no verbose mode\r\n\r\nQuality parameters\r\n-k (default 15): key size\r\n-c (default 0) : minimal size of contig\r\n-n (default 10): nail size\r\n-e (default 8) : errors per N bp\r\n\r\nOptional output parameters\r\n-A : Ouput analysis information including coverage and alignment.\r\n-G : skip output information for contig\/gene groups to xxx-groups.txt\r\n-P : skip output SNPs of contigs to xxx-snps.txt\r\n-O : output small overlaps (<24bp) inside contigs to xxx-overlaps.fa\r\n-L : output chimeric segments to xxx-delutions.fa\r\n\r\nExecution parameters\r\n-a : action 1: only building index files; action 2: save indices before assembly; action 3: action is to do assembly directly.\r\n-d : the directory of index files.\r\n-T : running threads of accelerating assembly\r\n\r\nHelp\r\n-h<\/pre>\n
3. Several examples of running EBARDenovo<\/h1>\n
1. Most simplest\r\n$ mono EBARDenovo.exe [-T 24] -o contigs.fasta read1.fq.gz read2.fq.gz\r\n\r\n2. Using two stages of indexing and assembly (used usually):\r\n$ mono EBARDenovo.exe -a 1 -d index -T 24 \\\r\n-c 200 -o contigs.fasta read1.fq.gz read2.fq.gz\r\n$ mono EBARDenovo.exe -a 3 -d index -T 24 \\\r\n-c 200 -o contigs.fasta read1.fq.gz read2.fq.gz\r\n\r\n3. With full calculation and parameters\r\n$ mono EBARDenovo.exe -A -a 2 -d index -T 24 \\\r\n-k 15 -c 200 -n 10 -e 8 -O -L \\\r\n-o contigs.fasta read1.fq.gz read2.fq.gz<\/pre>\n
4. \u6ce8\u610f\u4e8b\u9879<\/h1>\n
\u4f7f\u7528\u8be5\u8f6f\u4ef6\u5e94\u7528\u4e8e\u8f6c\u5f55\u7ec4\u7684De novo<\/em>\u7ec4\u88c5\uff0c\u8c8c\u4f3c\u8981\u6c42short reads\u7684\u957f\u5ea6\u8981\u4e00\u81f4\u3002
\n\u5f53\u4f7f\u7528\u7684reads\u6570\u636e\u91cf\u8fc7\u5927\u7684\u65f6\u5019\uff0c\u5bb9\u6613\u51fa\u9519\uff1a<\/p>\n
\r\nBuild indx (Bulks of 100000 spots) ...1 2 3 4 5 6 7 8 9 10 11 12 Too many heap sections: Increase MAXHINCR or MAX_HEAP_SECTS\r\nStacktrace:\r\n\r\n  at (wrapper managed-to-native) object.__icall_wrapper_mono_array_new_specific (intptr,int) <0xffffffff>\r\n  at BioAsia.GSLib.TxtNgsReader.RechargeBuf () <0x0003b>\r\n  at BioAsia.GSLib.TxtNgsReader.Peek () <0x000eb>\r\n  at BioAsia.GSLib.FastqNgsReader.ReadSeqLine () <0x00083>\r\n  at BioAsia.EbarDenovo.EbarIndexing.BuildIndicesAndPairs (System.Collections.Generic.List`1) <0x007ea>\r\n  at BioAsia.EbarDenovo.EbarIndexing.Build () <0x00283>\r\n  at BioAsia.EbarDenovo.Program.Main (string[]) <0x0021b>\r\n  at (wrapper runtime-invoke) .runtime_invoke_void_object (object,intptr,intptr,intptr) <0xffffffff>\r\n\r\nNative stacktrace:\r\n\r\n        mono() [0x495e64]\r\n        \/lib64\/libpthread.so.0(+0xf500) [0x7fd088d7a500]\r\n        \/lib64\/libc.so.6(gsignal+0x35) [0x7fd088a0a8e5]\r\n        \/lib64\/libc.so.6(abort+0x175) [0x7fd088a0c0c5]\r\n        mono() [0x5e8375]\r\n        mono() [0x5e0108]\r\n        mono() [0x5e058d]\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. How to Install EBARDenovo on Linux mo … \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":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1914"}],"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=1914"}],"version-history":[{"count":12,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1914\/revisions"}],"predecessor-version":[{"id":1964,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1914\/revisions\/1964"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1914"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1914"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1914"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}