{"id":2116,"date":"2014-06-09T21:37:06","date_gmt":"2014-06-09T13:37:06","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2116"},"modified":"2014-06-09T21:37:06","modified_gmt":"2014-06-09T13:37:06","slug":"%e4%bd%bf%e7%94%a8-spades-%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=2116","title":{"rendered":"\u4f7f\u7528 SPAdes \u8fdb\u884c\u57fa\u56e0\u7ec4\u7ec4\u88c5"},"content":{"rendered":"

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

SPAdes \u4e3b\u8981\u7528\u4e8e\u8fdb\u884c\u5355\u7ec6\u80de\u6d4b\u5e8f\u7684\u7ec6\u83cc\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u5f53\u7136\u4e5f\u80fd\u7528\u4e8e\u975e\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u3002\u8f93\u5165\u6570\u636e\u53ef\u4ee5\u662f Illumina\u3001IonTorrent reads,\u6216 PacBio\u3001Sanger reads\uff0c\u4e5f\u53ef\u4ee5\u628a\u4e00\u4e9b contigs \u5e8f\u5217\u4f5c\u4e3a long reads \u8fdb\u884c\u8f93\u5165\u3002\u8be5\u8f6f\u4ef6\u53ef\u4ee5\u540c\u65f6\u63a5\u53d7\u591a\u7ec4 paired-end\u3001mate-pairs \u548c unpaired reads \u6570\u636e\u7684\u8f93\u5165\u3002\u540c\u65f6\u8be5\u8f6f\u4ef6\u6709\u4e00\u4e2a\u72ec\u7acb\u7684\u6a21\u5757\u7528\u4e8e\u8fdb\u884c\u6742\u5408\u57fa\u56e0\u7ec4\u7684\u7ec4\u88c5\u3002
\n\u6587\u732e\uff1aBankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing[J]. Journal of Computational Biology, 2012, 19(5): 455-477.<\/a>
\n\u8f6f\u4ef6\u8bf4\u660e\u6587\u6863\uff1ahttp:\/\/spades.bioinf.spbau.ru\/release3.0.0\/manual.html#sec2.1<\/a>
\nSPAdes \u5305\u542b\u591a\u4e2a\u72ec\u7acb\u6a21\u5757\uff1a<\/p>\n

\r\nBayesHammer\uff1a \u7528\u4e8e Illumina reads \u7684\u4fee\u6b63\r\nIonHammer\uff1a \u7528\u4e8e IonTorrent \u6570\u636e\u7684\u4fee\u6b63\r\nSPAdes\uff1a \u7528\u4e8e\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff1bK \u503c\u662f\u8f6f\u4ef6\u81ea\u52a8\u9009\u62e9\u7684\u3002\r\nMismatchCorrector\uff1a \u5bf9\u7ec4\u88c5\u7ed3\u679c contigs \u6216 scaffolds \u7684 mismatch \u548c sort indels \u8fdb\u884c\u4fee\u6b63\uff1b\u6b64\u6a21\u5757\u9700\u8981\u4f7f\u7528 BWA\uff1b\u9ed8\u8ba4\u4e0b\u6b64\u6a21\u5757\u662f\u5173\u95ed\u7684\uff0c\u4f46\u662f\u63a8\u8350\u5f00\u542f\u5b83\u3002\r\ndipSPAdes\uff1a \u7528\u4e8e\u7ec4\u88c5\u53cc\u500d\u578b\u9ad8\u6742\u5408\u57fa\u56e0\u7ec4\uff1b\u66f4\u591a\u8bf4\u660e\uff1adipSPAdes manual<\/a>\r\n<\/pre>\n
2. SPAdes \u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n
\u4ece\u7f51\u9875http:\/\/bioinf.spbau.ru\/spades<\/a>\u4e0b\u8f7d\u9700\u8981\u586b\u5199\u4e00\u4e9b\u4e2a\u4eba\u8d44\u6599\u3002<\/p>\n
\r\n$ wget http:\/\/spades.bioinf.spbau.ru\/release3.1.0\/SPAdes-3.1.0-Linux.tar.gz\r\n$ tar -xzf SPAdes-3.1.0-Linux.tar.gz -C \/opt\/biosoft\/\r\n$ \/opt\/biosoft\/SPAdes-3.1.0-Linux\/bin\/spades.py --test\r\n\u6d4b\u8bd5\u8fd0\u884c\r\n<\/pre>\n
3. SPAdes \u7684\u4f7f\u7528<\/h1>\n
3.1 \u8f93\u5165\u6570\u636e<\/h2>\n
SPAdes 3.0.0 \u7684\u8fd0\u884c\u81f3\u5c11\u9700\u8981\u6709\u4ee5\u4e0b\u4e00\u79cd\u6570\u636e\uff1a<\/p>\n
\r\nIllumina paired-end\/unpaired reads\r\nIonTorrent paired-end\/unpaired reads\r\nPacBio CCS reads\r\n<\/pre>\n
\u5e76\u4e14\uff0c\u503c\u5f97\u6ce8\u610f\u7684\u662f\uff1aIllumina \u6570\u636e\u548c Ionorrent \u6570\u636e\u4e0d\u80fd\u540c\u65f6\u7528\u4e8e\u7ec4\u88c5\uff1b \u4ec5\u6709 mate-paired\uff0cPacBio CLR reads, Sanger reads \u6216 additional contigs \u6570\u636e\u65f6\uff0c\u4e0d\u5e94\u8be5\u4f7f\u7528 SPAdes \u8fdb\u884c\u7ec4\u88c5\u3002
\nSPAdes \u652f\u6301\u7684 Paired-end \u548c Mate-Paired \u7684\u6570\u636e\uff0c\u5176\u6570\u636e\u9700\u8981\u4e3a fastq \u683c\u5f0f\uff0c\u8f6f\u4ef6\u9700\u8981\u5bf9\u5176\u8fdb\u884c reads \u7684 error correction \u3002\u540c\u65f6\uff0c SPAdes \u4e5f\u652f\u6301\u4f7f\u7528 Sanger \u6216 PacBio CCS \u7684 reads \u6570\u636e\uff0c\u4f46\u8f6f\u4ef6\u4e0d\u80fd\u5bf9\u6b64\u6570\u636e\u8fdb\u884c error correction\u3002<\/p>\n
3.1.1 Read-pair \u6570\u636e<\/h3>\n
Read-pair \u6570\u636e\u8f93\u5165\u5230\u7a0b\u5e8f\u4e2d\u6709 3 \u79cd\u65b9\u5f0f\uff1a
\n1. left \u548c right \u7684 reads \u5206\u522b\u5728\u4e24\u4e2a fastq \u6587\u4ef6\u4e2d\u3002
\n2. left \u548c right \u7684 reads \u4ea4\u53c9\u878d\u5408\u5728\u4e00\u4e2a fastq \u6587\u4ef6\u4e2d\u3002
\n3. \u5c06\u6240\u6709\u7684\u8f93\u5165\u6570\u636e\u4fe1\u606f\u6574\u5408\u5728\u4e00\u4e2a YAML \u683c\u5f0f\u7684\u6587\u672c\u6587\u4ef6\u4e2d\u3002<\/p>\n
\u4f7f\u7528\u975e YAML \u65b9\u5f0f\u8f93\u5165\u6570\u636e\uff0c\u8fd9\u79cd\u65b9\u5f0f\u6700\u591a\u80fd\u4f7f\u7528 5 \u7ec4 paired-end \u6570\u636e \u548c 5 \u7ec4 mate-paired \u6570\u636e\u3002
\n\u4ec5\u6709\u4e00\u4e2a library \u6570\u636e\u65f6\uff1a<\/p>\n
\r\n--12 file_name\r\n12 \u8868\u793a\u540e\u9762\u63a5\u7684\u6587\u4ef6\u662f\u4ea4\u53c9\u878d\u5408\u7684 paired \u6570\u636e\uff0c\u4e0b\u540c\u3002\r\n-1 file_name\r\n1 \u8868\u793a left \u6570\u636e\r\n-2 file_name\r\n2 \u8868\u793a right \u6570\u636e\r\n-s file_name\r\ns \u8868\u793a single \u6570\u636e, \u4e5f\u7528\u4e8e\u8f93\u5165 PacBio CCS reads\u3002\r\n<\/pre>\n
\u6709\u591a\u4e2a paired-end library \u6570\u636e\u65f6\uff1a<\/p>\n
\r\n--pe{int}-12 \u7f16\u53f7\u4e3a int \u7684 library \u7684\u4ea4\u53c9\u878d\u5408\u540e\u7684 paired \u6570\u636e\u3002int \u53d6\u503c\u53ea\u80fd\u662f 1,2,3,4,5 \u3002\u4e0b\u540c\u3002\r\n--pe{int}-1  \u7f16\u53f7\u4e3a int \u7684 library \u7684 left \u6570\u636e\r\n--pe{int}-2  \u7f16\u53f7\u4e3a int \u7684 library \u7684 right \u6570\u636e\r\n--pe{int}-s  \u7f16\u53f7\u4e3a int \u7684 library \u7684 single \u6570\u636e\r\n--pe{int}-{fr|rf|ff} \u7f16\u53f7\u4e3a int \u7684 library \u7684\u6570\u636e\u7684\u65b9\u5411\uff0c\u9ed8\u8ba4\u4e3a --pe{int}-fr \u3002\r\n<\/pre>\n
\u6709\u591a\u4e2a mate-paired library \u6570\u636e\u65f6\uff1a<\/p>\n
\r\n--mp{int}-12 \u7f16\u53f7\u4e3a int \u7684 library \u7684\u4ea4\u53c9\u878d\u5408\u540e\u7684 paired \u6570\u636e\r\n--mp{int}-1  \u7f16\u53f7\u4e3a int \u7684 library \u7684 left \u6570\u636e\r\n--mp{int}-2  \u7f16\u53f7\u4e3a int \u7684 library \u7684 right \u6570\u636e\r\n--mp{int}-s  \u7f16\u53f7\u4e3a int \u7684 library \u7684 single \u6570\u636e\r\n--mp{int}-{fr|rf|ff} \u7f16\u53f7\u4e3a int \u7684 library \u7684\u6570\u636e\u7684\u65b9\u5411\uff0c\u9ed8\u8ba4\u4e3a --mp{int}-rf \u3002\r\n<\/pre>\n
3.1.2 PacBio \u6570\u636e<\/h3>\n
PacBio \u6570\u636e\u6709\u4e24\u79cd\uff1a CCS (circular consensus sequence) \u548c CLR (continuous long read)\u3002PacBio CLR \u6570\u636e\u6709\u5229\u4e8e\u6742\u5408\u57fa\u56e0\u7ec4\u7684\u7ec4\u88c5\u3002
\n\u6570\u636e\u8f93\u5165\u53c2\u6570\uff1a<\/p>\n
\r\n--pacbio  \u8f93\u5165 PacBio CLR reads\r\n--sanger  \u8f93\u5165 sanger reads\r\n<\/pre>\n
3.1.3 Additional contigs<\/h3>\n
\r\n--trusted-contigs\r\n\u8f93\u5165\u53ef\u4fe1\u5ea6\u9ad8\u7684 contigs\uff0c\u7528\u4e8e graph construction, gap closure \u548c repeat resolution\u3002\r\n--untrusted-contigs\r\n\u8f93\u5165\u53ef\u4fe1\u5ea6\u8f83\u4f4e\u7684 contigs, \u7528\u4e8egap closure \u548c repeat resolution\u3002\r\n<\/pre>\n
\u8fd9\u4e24\u4e2a\u53c2\u6570\u4e0d\u80fd\u8f93\u5165\u5176\u5b83\u90bb\u8fd1\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002\u4ec5\u7528\u4e8e\u8f93\u5165\u540c\u4e00\u4e2a\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u7684 contigs \u3002<\/p>\n
3.1.4 YAML \u65b9\u5f0f\u8f93\u5165\u6570\u636e<\/h3>\n
\r\n--dataset\r\nYAML \u683c\u5f0f\u7684\u6587\u4ef6\r\n<\/pre>\n
\r\n    [\r\n      {\r\n        orientation: \"fr\",\r\n        type: \"paired-end\",\r\n        right reads: [\r\n          \"\/FULL_PATH_TO_DATASET\/lib_pe1_right_1.fastq\",\r\n          \"\/FULL_PATH_TO_DATASET\/lib_pe1_right_2.fastq\"\r\n        ],\r\n        left reads: [\r\n          \"\/FULL_PATH_TO_DATASET\/lib_pe1_left_1.fastq\",\r\n          \"\/FULL_PATH_TO_DATASET\/lib_pe1_left_2.fastq\"\r\n        ]\r\n      },\r\n      {\r\n        orientation: \"rf\",\r\n        type: \"mate-pairs\",\r\n        right reads: [\r\n          \"\/FULL_PATH_TO_DATASET\/lib_mp1_right.fastq\"\r\n        ],\r\n        left reads: [\r\n          \"\/FULL_PATH_TO_DATASET\/lib_mp1_left.fastq\"\r\n        ]\r\n      },\r\n      {\r\n        type: \"single\",\r\n        single reads: [\r\n          \"\/FULL_PATH_TO_DATASET\/pacbio_ccs.fastq\"\r\n        ]\r\n      },\r\n      {\r\n        type: \"pacbio\",\r\n        single reads: [\r\n          \"\/FULL_PATH_TO_DATASET\/pacbio_clr.fastq\"\r\n        ]\r\n      }\r\n    ]\r\n<\/pre>\n
3.2 \u53c2\u6570<\/h2>\n
\u4f7f\u7528 spades.py \u8fd0\u884c SPAdes \u7a0b\u5e8f\uff1a<\/p>\n
\r\n$ \/opt\/biosoft\/SPAdes-3.0.0-Linux\/bin\/spades.py [options] -o output_dir\r\n<\/pre>\n
\u53c2\u6570\uff1a<\/p>\n
\r\n-o output_dir\r\n\u6307\u5b9a\u8f93\u51fa\u7684\u6587\u4ef6\u5939\r\n--sc\r\n\u6b64 flag \u7528\u4e8e MDA (single-cell) \u6570\u636e\r\n--iontorrent\r\n\u6b64 flag \u7528\u4e8e IonTorrent \u6570\u636e\u7684\u7ec4\u88c5\r\n--test\r\n\u4f7f\u7528 test \u6570\u636e\u8fd0\u884c SPAdes\uff0c\u7528\u4e8e\u68c0\u6d4b\u8f6f\u4ef6\u662f\u5426\u6b63\u786e\u5b89\u88c5\r\n-h | --help\r\n\u6253\u5370\u5e2e\u52a9\u4fe1\u606f\r\n--only-error-correction\r\n\u4ec5\u4ec5\u6267\u884c reads error correction \u6b65\u9aa4\r\n--only-assembler\r\n\u4ec5\u4ec5\u8fd0\u884c\u7ec4\u88c5\u6a21\u5757\r\n--careful\r\n\u901a\u8fc7\u8fd0\u884c MismatchCorrector \u6a21\u5757\u8fdb\u884c\u57fa\u56e0\u7ec4\u4e0a mismatches \u548c short indels \u7684\u4fee\u6b63\u3002\u63a8\u8350\u4f7f\u7528\u6b64\u53c2\u6570\u3002\r\n--continue\r\n\u4ece\u4e0a\u4e00\u6b21\u7ec8\u6b62\u5904\u7ee7\u7eed\u8fd0\u884c\u7a0b\u5e8f\u3002\r\n--restart-from\r\n\u4ece\u6307\u5b9a\u7684\u4f4d\u7f6e\u91cd\u65b0\u5f00\u59cb\u8fd0\u884c\u7a0b\u5e8f\u3002\u548c\u4e0a\u4e00\u4e2a\u53c2\u6570\u76f8\u6bd4\uff0c\u6b64\u53c2\u6570\u53ef\u4ee5\u7528\u4e8e\u6539\u53d8\u4e00\u4e9b\u7ec4\u88c5\u53c2\u6570\u3002\u53ef\u9009\u7684\u503c\u6709\uff1a\r\n\r\nec \u4ece error correction \u5904\u5f00\u59cb\r\nas \u4ece assembly module \u5904\u5f00\u59cb\r\nk{int} \u4ece\u6307\u5b9a\u7684 k \u503c\u5904\u5f00\u59cb\r\nmc \u4ece mismatch correction \u5904\u5f00\u59cb\r\n\r\n--disable-gzip-output\r\n\u4f7f\u7528\u6b64\u53c2\u6570\u6765\u8bbe\u5b9a\u4e0d\u5bf9 corrected reads \u8fdb\u884c\u538b\u7f29\u3002\u9ed8\u8ba4\u4e0b corrected reads \u662f .fastq.gz \u683c\u5f0f\u7684\r\n-t int\r\n\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\uff0c\u9ed8\u8ba4\u4e3a16\r\n-m int\r\n\u8bbe\u5b9a\u5185\u5b58\u7684\u9650\u5236\uff0c\u5355\u4f4d\u4e3a Gb\u3002\u5982\u679c\u7a0b\u5e8f\u4f7f\u7528\u7684\u5185\u5b58\u8fbe\u5230\u6b64\u503c\uff0c\u5219\u7a0b\u5e8f\u4f1a\u7ec8\u6b62\u8fd0\u884c\u3002\u9ed8\u8ba4\u503c\u662f 250 \u3002\r\n--tmp-dir dir_name\r\n\u8bbe\u7f6e reads error correction \u7684\u4e34\u65f6\u6587\u4ef6\u5b58\u653e\u8def\u5f84\u3002\u9ed8\u8ba4\u4e3a output_dir\/corrected\/tmp \u3002\r\n-k int,int,...\r\n\u7531\u9017\u53f7\u5206\u9694\u7684 k-mer sizes\u3002\u8fd9\u4e9b\u6570\u503c\u5fc5\u987b\u4e3a\u5947\u6570\uff0c\u8981\u5c0f\u4e8e 128\uff0c\u4e14\u6309\u5347\u5e8f\u6392\u5217\u3002\u5982\u679c\u4f7f\u7528\u4e86 --sc \u53c2\u6570\uff0c\u5219\u9ed8\u8ba4\u503c\u4e3a 21,33,55 \u3002 \u82e5\u6ca1\u6709 --sc \u53c2\u6570\uff0c\u5219\u7a0b\u5e8f\u4f1a\u6839\u636e reads \u957f\u5ea6\u81ea\u52a8\u9009\u62e9 k-mer \u53c2\u6570\u3002\r\n--phred-offset\r\n\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\uff0c 33 \u6216 64\r\n<\/pre>\n
3.3 \u5e38\u7528\u4f8b\u5b50<\/h2>\n
\u5355\u4e2a illumina paired-end \u6587\u5e93\uff1a<\/p>\n
\r\n$ spades.py -o output_dir -1 reads1.fastq -2 reads2.fastq\r\n<\/pre>\n
\u591a\u4e2a illumina paired-end \u548c mate-paired \u6587\u5e93\uff0c\u4ee5\u53ca Pcabio sanger contigs \u6570\u636e\uff1a<\/p>\n
\r\n$ spades.py -o output_dir\\\r\n --pe1-1 pe1_1.fq --pe1-2 pe1_2.fq --pe2-1 pe2_1.fq --pe2-2 pe2_2.fq\\\r\n --mp1-1 mp1_1.fq --mp1-2 mp1_2.fq --mp2-1 mp2_1.fq --mp2-2 mp2_2.fq\\\r\n -s pacibo_ccs.fastq --pacbio pacbio_clr.fastq\\\r\n --sanger sanger.fa\\\r\n --trusted-contigs trusted_contig.fa\\\r\n --untrusted-contigs untrusted_contig.fa\\\r\n --careful -t 16 --phred-offset 33 -m 250 -k 21,33,55 [--sc]\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. SPAdes \u7b80\u4ecb SPAdes \u4e3b\u8981\u7528\u4e8e\u8fdb\u884c\u5355\u7ec6\u80de\u6d4b\u5e8f\u7684\u7ec6\u83cc\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c … \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\/2116"}],"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=2116"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2116\/revisions"}],"predecessor-version":[{"id":2117,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2116\/revisions\/2117"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2116"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2116"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2116"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}