Velvet<\/a>\u7528\u4e8e\u57fa\u56e0\u7ec4\u7684de novo\u7ec4\u88c5\uff0c\u652f\u6301\u5404\u79cd\u539f\u59cb\u6570\u636e\uff0c\u5305\u62ecIllumina\u7684short reads\u548c454\u7684long reads\u3002<\/p>\n \u9996\u5148\u4e0b\u8f7dvelvet\u7684\u5b89\u88c5\u5305\uff0c\u76f4\u63a5\u4f7f\u7528make\u547d\u4ee4\u6765\u7f16\u8bd1\uff0c\u5373\u53ef\u83b7\u5f97\u53ef\u6267\u884c\u4e3b\u7a0b\u5e8fvelveth\u548cvelvetg\u3002\u5b89\u88c5\u5982\u4e0b\uff1a<\/p>\n \u503c\u5f97\u6ce8\u610f\u7684\u662f\uff0cmake\u540e\u6709\u591a\u79cd\u53c2\u6570\uff0c\u9700\u8981\u5bf9velvet\u8f6f\u4ef6\u8fdb\u884c\u9700\u8981\u7684\u8bbe\u7f6e\uff1a<\/p>\n CATEGORIES=10\uff1a<\/span> \u9ed8\u8ba4\u60c5\u51b5\u4e0bvelvet\u53ea\u80fd\u8f93\u5165 2 groups of short reads\uff0c\u6b64\u5904\u8bbe\u7f6e\u4e3a10. \u5982\u679c\u6709\u591a\u4e2a\u6587\u5e93\u6216\u591a\u79cd\u7c7b\u578b\u7684\u539f\u59cb\u6570\u636e\uff0c\u9700\u8981\u76f8\u5e94\u589e\u52a0\u8be5\u503c\u7684\u5927\u5c0f\u3002\u8be5\u503c\u8d8a\u5927\uff0c\u8017\u5185\u5b58\u8d8a\u5927\u3002<\/p>\n MAXKMERLENGTH=57\uff1a<\/span> \u6700\u5927\u7684Kmer\u957f\u5ea6\uff0c\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u8be5\u503c\u4e3a 31\uff0c \u4e00\u822cde novo\u7ec4\u88c5\u57fa\u56e0\u7ec4\uff0c31 \u662f\u4e0d\u591f\u7684\uff0c\u6545\u9700\u8981\u589e\u5927\u8be5\u503c\u3002\u7ec4\u88c5\u8fc7\u7a0b\u4e2dkmer\u8d8a\u5927\uff0c\u8d8a\u8017\u5185\u5b58\u3002<\/p>\n BIGASSEMBLY=1\uff1a<\/span> \u5f53\u8d85\u8fc7 2.2G \u7684reads\u7528\u4e8e\u7ec4\u88c5\u57fa\u56e0\u7ec4\u7684\u65f6\u5019\uff0c\u9700\u8981\u8bbe\u7f6e\u8be5\u503c\u3002\u5b9e\u9645\u4e0a\u5f88\u5c11\u4f1a\u6709\u5982\u6b64\u4e4b\u591a\u7684reads\u7528\u4e8e\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u53ef\u4ee5\u4e0d\u7528\u8bbe\u7f6e\u8be5\u503c\u3002\u8bbe\u7f6e\u8be5\u503c\u540e\uff0c\u4f1a\u6d88\u8017\u66f4\u591a\u7684\u5185\u5b58\u3002<\/p>\n LONGSEQUENCES=1\uff1a<\/span> \u5f53\u7ec4\u88c5\u51fa\u7684contigs\u957f\u5ea6\u8d85\u8fc7 32kb \u957f\u7684\u65f6\u5019\uff0c\u9700\u8981\u8bbe\u7f6e\u8be5\u503c\u3002\u4f1a\u6d88\u8017\u8ddf\u591a\u5185\u5b58\u3002<\/p>\n OPENMP=1<\/span>\uff1a\u6253\u5f00\u591a\u7ebf\u7a0b\u8fd0\u884c\u3002\u9700\u8981\u8bbe\u7f6e\u73af\u5883\u53d8\u91cf OMP_NUM_THREADS \u548c OMP_THREAD_LIMIT\u3002 Velvet\u6700\u591a\u4f7f\u7528 OMP_NUM_THREADS+1 \u6216 OMP_THREAD_LIMIT \u4e2a\u7ebf\u7a0b\u3002\u4e5f\u503c\u54df\u90e8\u5206\u7684velvet\u7b97\u6cd5\u652f\u6301\u591a\u7ebf\u7a0b\u8fd0\u884c\uff0c\u4e0d\u4f1a\u9020\u6210\u8fd0\u884c\u65f6\u95f4\u7684\u7ebf\u6027\u51cf\u5c11\u3002<\/p>\n BUNDLEDZLIB=1\uff1a<\/span> \u9ed8\u8ba4velvet\u4f7f\u7528\u7cfb\u7edf\u81ea\u5e26\u7684zlib\uff0c\u5982\u679c\u7cfb\u7edf\u6ca1\u6709zlib\uff0c\u5219\u9700\u8981\u52a0\u5165\u8be5\u53c2\u6570\u6765\u4f7f\u7528velvet\u6e90\u7801\u5305\u4e2d\u81ea\u5e26\u7684zlib\u3002<\/p>\n \u5728\u4e0a\u8ff0 make \u7f16\u8bd1\u5b8c Velvet \u540e\uff0c\u7ee7\u7eedvelvet\u7684\u4f7f\u7528<\/p>\n velveth\u63a5\u53d7\u8f93\u5165\u7684\u6587\u4ef6\uff0c\u4ea7\u751f\u4e00\u4e2ahash\u8868\u3002\u751f\u6210\u4e24\u4e2a\u6587\u4ef6\uff1aSequences\u548cRoadmaps\u3002velveth\u7528\u6cd5\u4e3a\uff1a<\/p>\n \u5728\u4e0d\u5e26\u53c2\u6570\u60c5\u51b5\u4e0b\uff0c\u76f4\u63a5\u8fd0\u884cvelveth\u4f1a\u7ed9\u51fa\u5176\u5e2e\u52a9\u6587\u4ef6\u3002\u800c\u5176\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n output_directory\uff1a<\/span>\u8f93\u51fa\u6587\u4ef6\u5939\u7684\u8def\u5f84<\/p>\n hash_length\uff1a<\/span> \u8bbe\u7f6eKmer\u7684\u5927\u5c0f\u3002\u8be5\u503c3\u70b9\u8981\u6c42\uff1a1.\u5fc5\u987b\u4e3a\u5947\u6570\uff1b2.\u5fc5\u987b\u5c0f\u4e8e\u6216\u7b49\u4e8e\u7f16\u8bd1velvet\u65f6\u8bbe\u7f6e\u7684MAXKMERLENGTH\u503c\uff1b3.\u5fc5\u987b\u5c0f\u4e8ereads\u7684\u957f\u5ea6\u3002<\/p>\n file_format\uff1a<\/span> \u652f\u6301\u7684\u683c\u5f0f\u6709fasta\uff08\u9ed8\u8ba4\uff09\u3001fastq\u3001bam\u7b49\u3002<\/p>\n reads_type\uff1a<\/span> short(\u9ed8\u8ba4)\u3001shortpaired\u3001short2\u3001shortpaired2 … short10\u3001shortpaired10\u3001long\u3001longPaired\u3002 \u9ed8\u8ba4\u60c5\u51b5\u4e0bshort reads\u53ea\u4fdd\u7559\u4e862\u4e2a\u901a\u9053\u3002\u5728\u4e4b\u524d\u8bbe\u7f6e\u4e2d\u5c06CATEGORIES\u503c\u8bbe\u7f6e\u4e3a10\uff0c\u5219velvet\u6700\u591a\u652f\u630110\u79cd\u4e0d\u540c\u7c7b\u578b\u7684short reads\u6570\u636e\u3002long\u652f\u6301\u957f\u7684reads\uff0c\u6bd4\u5982sanger\u6d4b\u5e8f\u6570\u636e\u548c454\u6d4b\u5e8f\u6570\u636e\u3002 \u5982\u679creads_type\u4e00\u81f4\uff0c\u5219\u540c\u4e00\u4e2areads_type\u4e0b\u53ef\u4ee5\u6709\u591a\u4e2a\u6587\u4ef6\u3002<\/p>\n filename1\uff1a<\/span> reads\u7684\u6587\u4ef6\u540d\u3002\u5982\u679c\u662f\u6210\u5bf9\u7684reads\uff0c\u5219\u9700\u8981\u5c06\u4e24\u4e2areads\u6587\u4ef6\u5408\u5e76\u6210\u4e00\u4e2a\u6587\u4ef6\u3002Velvet\u5b89\u88c5\u6587\u4ef6\u5939\u4e2d\u63d0\u4f9b\u4e86\u8fd9\u6837\u7684\u4e00\u4e2a\u6587\u4ef6\u3002<\/p>\n \u4e00\u4e2avelveth\u7684\u4f8b\u5b50\u3002\u5bf95\u4e2aIllumina\u6d4b\u5e8f\u7684\u7ed3\u679c\u548c\u4e00\u4e2a454\u6d4b\u5e8f\u7684\u7ed3\u679c\u4f7f\u7528velvet\u8fdb\u884c\u7ec4\u88c5\uff1a<\/p>\n velvetg\u662fvlevet\u8f6f\u4ef6\u7684\u8fdb\u884cde Bruijin\u56fe\u6784\u5efa\u548c\u64cd\u4f5c\u7684\u6838\u5fc3\u3002\u5728\u547d\u4ee4\u884c\u4e0b\u76f4\u63a5\u952e\u5165\u547d\u4ee4velvetg\uff0c\u8fd9\u6837\u63cf\u8ff0\uff1avelvetg – de Bruijn graph construction, error removal and repeat resolution\u3002\u5176\u4f7f\u7528\u65b9\u6cd5\u5982\u4e0b\uff1a<\/p>\n directory \u5de5\u4f5c\u7684\u76ee\u5f55\u540d\uff0c\u5373\u4e3a\u4e0a\u4e00\u6b65\u9aa4velveth\u4e2d\u7684\u8f93\u51fa\u6587\u4ef6\u5939\u3002<\/p>\n -cov_cutoff <float|auto> default\uff1a no removal<\/span> -exp_cov <float|auto> default\uff1a no long or paired-end read resolution\u3002<\/span> -long_cov_cutoff <float> default\uff1a no removal<\/span> -ins_length <interger><\/span> -ins_length* <interger><\/span> -ins_length_long <interger><\/span> -ins_length*_sd <interger><\/span> -scaffolding <yes|no> defautl: yes<\/span> -max_branch_length <integer> default: 100 -max_divergence <float> default: 0.2 -max_gap_count <integer> default: 3 -min_pair_count <integer> default: 5 -long_mult_cutoff <integer> default: 2 -max_coverage <float> default: no removal -coverage_mask <integer> default: 1 -shortMatePaired* <yes|no> default: no<\/span> -conserveLong <yes|no> default: no -unused_reads <yes|no> default: no -alignments <yes|no> default: no -exportFiltered <yes|no> default: no -clean <yes|no> default: no<\/span> -very_clean <yes|no> default: no -min_contig_lgth <integer> default: hash length * 2 -amos_file <yes|no> default: no directory\/contigs.fa \u957f\u5ea62\u500d\u957f\u4e8ekmer\u7684contigs\u3002\u53c2\u6570-scaffolding\u51b3\u5b9a\u751f\u6210\u7684\u8be5fasta\u6587\u4ef6\u662f\u5426\u5305\u542bscaffold\u5e8f\u5217\u3002 \u8fd9\u4e9bscripts\u975e\u5e38\u6709\u7528\uff0c\u4f4d\u4e8e$velvetHome\/contrib\/\u6587\u4ef6\u5939\u4e0b\u3002<\/p>\n \u5728\u4f7f\u7528velvetg\u7ec4\u88c5\u51fa\u4e00\u4e2a\u521d\u6b65\u7ed3\u679c\u540e\uff0c\u5229\u7528\u7ed3\u679c\u6587\u4ef6stats.txt\u6765\u4f30\u7b97\u51fakmer\u7684\u671f\u671b\u8986\u76d6\u5ea6\u3002<\/p>\n \u5728\u4f7f\u7528velvetg\u7ec4\u88c5\u51fa\u4e00\u4e2a\u521d\u6b65\u7ed3\u679c\u540e\uff0c\u4ee5\u7ed3\u679c\u6587\u4ef6\u5939\u4e3a\u8f93\u5165\uff0c\u8ba1\u7b97insert size\u548cinsert sd\u3002<\/p>\n \u5c06\u5bf9\u79f0\u7684reads1\u548creads2\u6587\u4ef6\u5408\u5e76\u6210\u4e00\u4e2a\u6587\u4ef6\uff0c\u7528\u4e8evelvet\u7684\u8f93\u5165\u3002velvet\u4e0d\u80fd\u5c06\u4e24\u4e2a\u6587\u4ef6\u7528\u4e8e\u8f93\u5165\u3002<\/p>\n \u8f93\u5165\u8be5\u811a\u672c\u7684\u547d\u4ee4\uff0c\u4e0d\u52a0\u53c2\u6570\uff0c\u7ed9\u51fa\u8be6\u7ec6\u7684\u5e2e\u52a9\u4fe1\u606f\u3002\u8be5\u7a0b\u5e8f\u7528\u4e8e\u9009\u53d6\u4e0d\u540c\u7684Kmer\u503c\uff0c\u6765\u5bf9\u539f\u59cb\u6570\u636e\u8fdb\u884c\u7ec4\u88c5\uff0c\u540c\u65f6\u8ba1\u7b97\u51fa\u6700\u4f18\u5316\u7684\u7ec4\u88c5\u53c2\u6570\u3002\u6700\u540e\u7ed9\u51fa\u6700\u4f18\u5316\u65b9\u6848\u7684\u7ec4\u88c5\u7ed3\u679c\u3002\u975e\u5e38\u9002\u5408\u4e8e\u7b80\u5355\u57fa\u56e0\u7ec4\u7684\u81ea\u52a8\u5316\u7ec4\u88c5\u64cd\u4f5c\u3002\u5176\u53c2\u6570\u8bbe\u7f6e\u8f83\u4e3a\u7b80\u5355\u3002\u5f53\u7136\u9700\u8981\u80fd\u5728$PATH\u4e2d\u6709velveth\u548cvelvetg\u4e24\u4e2a\u4e3b\u8981\u7684velvet\u547d\u4ee4\u3002\u4ee5\u4e0b\u5c31\u4e0d\u8be6\u7ec6\u4ecb\u7ecd\u8be5\u547d\u4ee4\u53c2\u6570\uff0c\u4ec5\u7ed9\u51fa\u4e00\u4e2a\u4f8b\u5b50:<\/p>\n \u4ee5\u4e0a\u547d\u4ee4\u610f\u4e49\u4e3a\uff1a\u4f7f\u7528kmer\u957f\u5ea6\u4ece17\u523097\uff0c\u6bcf\u6b21\u8fd0\u884ckmer\u957f\u5ea6+2\uff1b –a\u8868\u793a\u8981\u751f\u6210amosfile\uff1b\u4f7f\u7528N50\u6765\u51b3\u5b9akmer\u7684\u9009\u53d6\uff1b\u4ee5’Lbp’,\u5373\u5927\u4e8e1kb\u7684contigs\u7684\u603b\u78b1\u57fa\u6570\u6765\u51b3\u5b9acoverage cutoff\u7684\u503c\u7684\u9009\u53d6\uff1b–f\u540e\u4e3avelveth\u7684\u53c2\u6570\uff1b–o\u540e\u63a5velvetg\u7684\u53c2\u6570\uff1b-g\u540e\u4e3a\u9884\u8ba1\u7684\u57fa\u56e0\u7ec4\u5927\u5c0f\uff0c\u7528\u4e8e\u8ba1\u7b97\u8be5\u547d\u4ee4\u4e0b\u5185\u5b58\u7684\u6d88\u8017\uff0c\u7136\u540e\u9000\u51fa\u8fd0\u884c\uff0c\u7531\u4e8e\u8be5\u7a0b\u5e8f\u4f1a\u540c\u65f6\u8fd0\u884c\u591a\u4e2avelvet\u548cvelveg\uff0c\u6d88\u8017\u7684\u5185\u5b58\u5de8\u5927\u3002<\/p>\n \u8be5\u7a0b\u5e8f\u80fd\u4f7f\u7528\u4e0d\u540c\u7684kmer\u7ec4\u88c5\u51fa\u5f88\u591aAssemblies\uff0c\u7136\u540e\u5c06\u8fd9\u4e9bAssemblies\u7ec4\u88c5\u878d\u5408\u51fa\u4e00\u4e2a\u6700\u7ec8\u7684\u7ed3\u679c\u3002\u5176\u4f7f\u7528\u65b9\u6cd5\u4f4d\u4e8e\u8be5\u7a0b\u5e8f\u7684\u901a\u76ee\u5f55\u4e0b\u7684README\u6587\u672c\u6587\u4ef6\u4e2d\u3002\u7ed9\u51fa\u4e00\u4e2a\u4f8b\u5b50\u5982\u4e0b\uff1a<\/p>\n \u4ee5\u4e0a\u547d\u4ee4\u610f\u4e49\u4e3a\uff1a\u4f7f\u7528\u4ece17\u523099\u7684kmer\uff0c\u6bcf\u79cdkmer\u90fd\u7ec4\u88c5\u51fa\u57fa\u56e0\u7ec4\u5e76\u6700\u540e\u5408\u5e76\u6210\u4e00\u4e2a\u7ed3\u679c\u3002-c\u4e3acoverage cutoff\u503c\uff1b-t\u8bbe\u7f6e\u4e3a\u53ea\u6709\u5927\u4e8e35\u7684kmer\u65f6\uff0c\u624d\u8fdb\u884ccoverage cutoff\uff1b-i\u8868\u793a\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u4e3a300\uff1b-m\u8868\u793a\u671f\u671b\u7684kmer\u8986\u76d6\u5ea6\u4e3a51\uff1b-r\u8868\u793a\u7ed3\u679c\u7ed9\u51fashort reads\u8981\u5305\u542b\u5230\u6700\u540e\u7684\u7ec4\u88c5\u7ed3\u679c\u4e2d\u3002<\/p>\n \u53ef\u4ee5\u770b\u51fa\u8be5\u7a0b\u5e8f\u9002\u5408\u4e8e\u53ea\u6709\u4e00\u79cd\u7c7b\u578b\u7684short reads\u65f6\uff0c\u624d\u9002\u5408\u3002\u56e0\u4e3a\u5176\u53c2\u6570-i\u53ea\u80fd\u8bbe\u7f6e\u4e00\u79cd\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u5927\u5c0f\u3002<\/p>\n extractContigReads\u7528\u4e8e\u63d0\u53d6\u548c\u6307\u5b9aconting\u76f8\u5bf9\u5e94\u7684reads\uff1b<\/p>\n afg_handing \u7528\u4e8e\u68c0\u67e5 .afg \u6587\u4ef6\uff1b<\/p>\n fasta2agp \u7528\u4e8e\u5c06fasta\u683c\u5f0f\u7684\u57fa\u56e0\u7ec4\u7ec4\u88c5\u7ed3\u679c(gaps\u7528N\u8868\u793a)\u8f6c\u6362\u6210AGP\u6587\u4ef6\uff0c\u7528\u4e8e\u63d0\u4ea4\u5230EMBL\u6216NCBI\uff1b<\/p>\n show_repeats \u6307\u51faAssembly\u4e2dlarger repeated contigs\u7684\u957f\u5ea6\uff1b<\/p>\n read_prepare \u548c select_paired \u7528\u4e8eNGS\u6570\u636e\u7684\u8fc7\u6ee4<\/p>\n 1. Velvet\u7684\u5b89\u88c5 Velvet\u7528\u4e8e\u57fa\u56e0\u7ec4\u7684de novo\u7ec4\u88c5\uff0c\u652f\u6301\u5404\u79cd\u539f … \u7ee7\u7eed\u9605\u8bfb $ wget http:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/velvet_1.2.10.tgz\r\n$ tar zxf velvet_1.2.10.tgz\r\n$ cd velvet_1.2.10\r\n$ make 'CATEGORIES=10' 'MAXKMERLENGTH=57' 'LONGSEQUENCES=1' \\\r\n 'OPENMP=1' 'BUNDLEDZLIB=1'<\/pre>\n
2. \u4f7f\u7528velveth\u6765\u51c6\u5907\u6570\u636e<\/h2>\n
$ velveth\r\n$ velveth output_directory hash_length \\\r\n -file_format -read_type filename1 filename2 ... \\\r\n [-file_format -read_type filename1 filename2 ...]<\/pre>\n
$ velveth output\/ 31 \\\r\n -shortPaired -fastq fragment1.reads.fastq \\\r\n -shortPaired2 -fastq fragment2.reads.fastq \\\r\n -shortPaired3 -fastq jumping1.reads.fastq \\\r\n -shortPaired4 -fastq jumping2.reads.fastq \\\r\n -long -fastq 454.fasta<\/pre>\n
3. \u4f7f\u7528velvetg\u6765\u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5<\/h1>\n
$ velvetg\r\n$ velvetg directory [options]\r\n\r\n$ velvetg output -exp_cov auto -cov_cutoff auto \\\r\n -shortMatePaired3 yes -shortMatePaired4 yes \\\r\n -clean yes -scaffolding yes -amos_file yes\r\n<\/pre>\n
velvetg\u7684\u5177\u4f53\u53c2\u6570\u5982\u4e0b\uff1a<\/h2>\n
\n\u8bbe\u7f6e\u6700\u4f4ekmer\u8986\u76d6\u5ea6\u7684\u503c\u3002\u9ed8\u8ba4\u4e0b\u4f1a\u751f\u6210\u5f88\u591anodes\uff0c\u800c\u6709\u4e9bnodes\u5f88\u77ed\uff0c\u8986\u76d6\u5ea6\u8f83\u4f4e\uff0c\u9700\u8981\u53bb\u9664\u6389\u3002auto\u5219\u81ea\u52a8\u8bbe\u7f6e\u8be5\u503c\uff0c\u662f\u8be5\u503c\u4e3a\u6240\u6709nodes\u7684kmer\u8986\u76d6\u5ea6\u503c\u7684median\u503c\u76841\/2\u3002<\/p>\n
\n\u671f\u671b\u7684kmer\u8986\u76d6\u5ea6\u3002\u5982\u679c\u8bbe\u7f6e\u4e86auto\uff0c\u5219\u8be5\u503c\u4e3a\u6240\u6709nodes\u7684kmer\u8986\u76d6\u5ea6\u503c\u7684median\u503c; \u8be5\u503c\u8bbe\u7f6e\u4e3aauto\uff0c\u5219\u540c\u65f6\u81ea\u52a8\u8bbe\u7f6e-cov_cutoff\u4e3aauto\u3002\u5982\u679c\u5bf9\u6742\u5408\u57fa\u56e0\u7ec4\u8fdb\u884c\u7ec4\u88c5\u65f6\uff0c\u8bbe\u7f6eauto\uff0c\u5374\u5f88\u96be\u8fdb\u884c\u9884\u6d4b\uff0c\u7ec4\u88c5\u7ed3\u679c\u80af\u5b9a\u4e0d\u597d\u3002auto\u9002\u7528\u4e8e\u6807\u51c6\u7684\u57fa\u56e0\u7ec4\u6d4b\u5e8f\u3002<\/p>\n
\n\u79fb\u9664\u4f4elong-read\u8986\u76d6\u5ea6\u7684nodes\u3002<\/p>\n
\n\u6210\u5bf9\u7684short reads\u95f4\u7684distance\u7684\u671f\u671b\u503c\uff0c\u5373\u63d2\u5165\u7247\u6bb5\u7684\u5e73\u5747\u957f\u5ea6\u3002<\/p>\n
\n*\u4ee3\u8868\u7b2c*\u7ec4shortPaired reads, \u548c velveth \u4e2d\u7684\u53c2\u6570\u76f8\u5bf9\u5e94\u3002<\/p>\n
\n\u548c\u524d\u4e24\u4e2a\u53c2\u6570\u4e00\u6837\uff0c\u4ee3\u8868longPaired reads\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u3002<\/p>\n
\n\u6b64\u65f6’*’\u4ee3\u8868’nothing\u30012\u30013…\u3001long’\u7b49\uff0c\u548c\u4e0a\u9762\u76843\u4e2a\u53c2\u6570\u76f8\u5339\u914d\uff1b\u8be5\u503c\u8bbe\u7f6e\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u7684\u6807\u51c6\u5dee\u3002\u6709\u5173\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\u548csd\u7684\u5982\u679c\u4e0d\u8bbe\u7f6e\uff0cvelvet\u5219\u4f1a\u81ea\u52a8\u8ba1\u7b97\u3002velvet\u662f\u5c06\u6210\u5bf9\u7684reads\u6bd4\u5bf9\u5230\u7ec4\u88c5\u51fa\u6765\u7684nodes\u4e0a\uff0c\u6700\u540e\u8ba1\u7b97\u51fa\u4e00\u4e2ainsert size \u548csd\u3002\u8fd9\u6837\u505a\u7684\u8bdd\uff0c\u53ef\u80fd\u4f30\u7b97\u7684\u4e0d\u51c6\u786e\uff0c\u9700\u8981\u770bvelvet\u7684\u8fd0\u884c\u8f93\u51fa\u4fe1\u606f\uff0c\u68c0\u6d4b\u5176\u9884\u7b97\u662f\u5426\u51c6\u786e\u3002<\/p>\n
\n\u662f\u5426\u8981\u4f7f\u7528paired end\u4fe1\u606f\u8fdb\u884cscaffolds\u7ec4\u88c5<\/p>\n
\n\u5904\u7406\u6c14\u6ce1(bubble)\u7684\u53c2\u6570\u3002\u9ed8\u8ba4\u4e0b\uff0c\u5982\u679c\u4e24\u6761\u5e8f\u5217\u8d85\u8fc7\u4e86100bp\u7684\u4f4d\u70b9\u5904\u7684kmer\u4e0d\u4e00\u81f4\uff0c\u5219\u5c06\u8fd9\u4e24\u6761\u5e8f\u5217\u5206\u5f00\u6210\u5355\u72ec\u7684contigs\u3002<\/p>\n
\n\u5728\u4e00\u4e2abubble\u5185\u4e24\u6761branches\u6700\u5927\u7684\u5dee\u5f02\u7387\uff08\u5206\u6bcd\u4e3a\u8f83\u957f\u7684branch\u7684\u957f\u5ea6\uff09\u3002<\/p>\n
\n\u5728\u4e00\u4e2abubble\u5185\u4e24\u6761branches\u6bd4\u5bf9\u7ed3\u679c\u4e2d\uff0c\u8fd0\u884c\u7684\u6700\u5927gap\u6570\u3002\u8be5\u53c2\u6570\u548c\u4e0a\u4e24\u4e2a\u53c2\u6570\u4e3a\u91cd\u8981\u7684\u53c2\u6570\uff0c\u80fd\u5f88\u5927\u7a0b\u5ea6\u4e0a\u5f71\u54cd\u7ec4\u88c5\u7ed3\u679c\u3002\u5982\u679c\u8bbe\u7f6e\u5f97\u677e\u70b9\uff0c\u53ef\u5206\u522b\u5c06\u503c\u8bbe\u4e3a200,0.33,5\u3002<\/p>\n
\n\u9ed8\u8ba4\uff0c\u5c06\u4e24\u4e2acontigs\u8fde\u6210scaffold\u6700\u5c11\u9700\u89815\u5bf9paired reads\u7684\u9a8c\u8bc1\u3002\u5982\u679c\u6d4b\u5e8f\u6df1\u5ea6\u8f83\u5927\uff0c\u5219\u53ef\u4ee5\u63d0\u9ad8\u8be5\u503c\uff1b\u6d4b\u5e8f\u6df1\u5ea6\u4f4e\uff0c\u5219\u964d\u4f4e\u8be5\u503c\u3002<\/p>\n
\n\u9ed8\u8ba4\u4e0b\uff0c\u878d\u5408\u4e24\u4e2acontigs\u9700\u8981\u6700\u5c11\u67092\u4e2along reads\u9a8c\u8bc1\u3002<\/p>\n
\n\u6700\u9ad8\u7684\u8986\u76d6\u5ea6\uff0c\u9ad8\u4e8e\u6b64\u8986\u76d6\u5ea6\u7684nodes\u5c06\u88ab\u5220\u9664\u3002<\/p>\n
\ncontigs\u6700\u5c0f\u7684\u7f6e\u4fe1\u8986\u76d6\u5ea6\uff0c\u4f4e\u4e8e\u6b64\u8986\u76d6\u5ea6\u7684contigs\u88abmaksed\u3002<\/p>\n
\n\u5982\u679c\u54ea\u4e00\u4e2ashortPaired\u4e3amate-pair library\u6d4b\u5e8f\u7684\u7ed3\u679c\uff0c\u5219\u9700\u8981\u6307\u5b9a\u8be5\u53c2\u6570\u4e3ayes\u3002<\/p>\n
\n\u662f\u5426\u4fdd\u7559\u542b\u6709long reads\u7684\u5e8f\u5217<\/p>\n
\n\u662f\u5426\u8f93\u51faunused reads, \u4fdd\u5b58\u5230 UnusedReads.fa \u4e2d\u3002<\/p>\n
\n\u662f\u5426\u8f93\u51facontig\u6bd4\u5bf9\u5230\u53c2\u8003\u5e8f\u5217\u7684summary.<\/p>\n
\n\u662f\u5426\u8f93\u51fa\u7531\u4e8e\u8986\u76d6\u5ea6\u7684\u539f\u56e0\u88ab\u8fc7\u6ee4\u6389\u7684long nodes\u3002<\/p>\n
\n\u662f\u5426\u5220\u9664\u6240\u6709\u7684\u4e0d\u80fd\u7528\u4e8e\u91cd\u65b0\u8ba1\u7b97\u7684\u4e2d\u95f4\u6587\u4ef6<\/p>\n
\n\u662f\u5426\u5220\u9664\u6240\u6709\u7684\u4e2d\u95f4\u6587\u4ef6\uff08\u5220\u9664\u540e\u4e0d\u80fd\u91cd\u65b0\u8ba1\u7b97\uff09<\/p>\n
\n\u8f93\u51fa\u7ed3\u679c\u4e2d\u6700\u5c0f\u7684contigs\u957f\u5ea6<\/p>\n
\n\u662f\u5426\u8f93\u51faAMOS\u6587\u4ef6<\/p>\nvelvetg\u7684\u9ed8\u8ba4\u8f93\u51fa\u7ed3\u679c<\/h2>\n
\ndirectory\/stats.txt \u7528\u4e8e\u51b3\u5b9a\u8986\u76d6\u5ea6cutoff\u7684\u7edf\u8ba1\u8868
\ndirectory\/PreGraph \u521d\u59cb\u7684de vruijin\u56fe
\ndirectory\/Graph2 \u6700\u7ec8\u7684de bruijin\u56fe \u5173\u4e8e\u8be5\u6587\u4ef6\u4e2d\u5185\u5bb9\u7684\u89e3\u91ca\uff0c\u8bf7\u89c1velvet PDF manual\u3002
\ndirectory\/velvet_asm.afg AMOS\u517c\u5bb9\u7684\u7ec4\u88c5\u6587\u4ef6\uff0c\u80fd\u7528\u4e8eAMOS<\/a>\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8f6f\u4ef6\u5305
\ndirectory\/Log velvet\u7684\u8fd0\u884c\u8bb0\u5f55<\/p>\n4. Velvet\u63d0\u4f9b\u4e86\u989d\u5916\u7684\u4e00\u4e9bscripts<\/h1>\n
4.1 estimate-exp_cov<\/h1>\n
\r\n$ $velvetHome\/contrib\/estimate-exp_cov\/velvet-estimate-exp_cov.pl \\\r\n [options] stats.txt\r\n<\/pre>\n
4.2 observed-insert-length.pl<\/h2>\n
\r\n$ $velvetHome\/contrib\/observed-insert-length.pl\/observed-insert-length.pl \\\r\n [options] Velvet_directory\r\n<\/pre>\n
4.3 shuffleSequences<\/h2>\n
\r\n$ $velvetHome\/contrib\/shuffleSequences_fasta\/shuffleSequences_fastq.pl \\\r\n reads1.fastq reads2.fastq reads.fastq\r\n<\/pre>\n
4.4 VelvetOptimiser<\/h2>\n
\r\n$ $velvetHome\/contrib\/VelvetOptimiser-2.2.4\/VelvetOptimiser.pl \\\r\n --s 17 --e 97 --x 2 --a --t 4 --k 'n50' --c 'Lbp' \\\r\n --f '-shortPaired -fastq fragment1.reads.fastq \\\r\n -shortPaired2 -fastq fragment2.reads.fastq \\\r\n -shortPaired3 -fastq jumping1.reads.fastq \\\r\n -shortPaired4 -fastq jumping2.reads.fastq \\\r\n -long -fastq 454.fasta' \\\r\n -o 'shortMatePaired3 yes shortMatePaired4 yes' \\\r\n [-g 40M]\r\n<\/pre>\n
4.5 AssemblyAssembler<\/h2>\n
\r\n$ $velvetHome\/contrib\/AssemblyAssembler1.3\/AssemblyAssembler1.3.py \\\r\n -s 17 -e 99 -v $velvetHome -c 5.1 -t 35 -i 300 -m 51 -r y \\\r\n -f \"-fastq -shortPaired reads.fastq\"\r\n<\/pre>\n
4.6 \u5176\u5b83\u7a0b\u5e8f<\/h2>\n
5. \u6709\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0bvelvet\u7684\u7ec4\u88c5<\/h1>\n","protected":false},"excerpt":{"rendered":"