{"id":491,"date":"2020-04-27T15:15:07","date_gmt":"2020-04-27T07:15:07","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=491"},"modified":"2020-04-27T15:15:07","modified_gmt":"2020-04-27T07:15:07","slug":"lachesis%e5%ae%89%e8%a3%85%e5%8f%8a%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=491","title":{"rendered":"LACHESIS\u5b89\u88c5\u53ca\u4f7f\u7528"},"content":{"rendered":"<p>\u5728\u7ec4\u88c5\u57fa\u56e0\u7ec4\u65f6\uff0c\u4f7f\u7528\u4e8c\u4ee3\u6216\u4e09\u4ee3\u6570\u636e\u7ec4\u88c5\u5230contigs\u540e\uff0c\u4e0b\u4e00\u6b65\u5c31\u662f\u5c06contig\u63d0\u5347\u5230\u67d3\u8272\u4f53\u6c34\u5e73\u3002\u5982\u679c\u5229\u7528HiC\u6570\u636e\uff0c\u90a3\u4e48\u76ee\u524d\u5e38\u89c1\u7684\u7ec4\u88c5\u8f6f\u4ef6\u6709\u4e0b\u9762\u51e0\u4e2a\uff1a<\/p>\n<p><a href=\"https:\/\/github.com\/DovetailGenomics\/HiRise_July2015_GR\">HiRise<\/a>: 2015\u5e74\u540e\u7684GitHub\u5c31\u4e0d\u518d\u66f4\u65b0<br \/>\n<a href=\"https:\/\/github.com\/shendurelab\/LACHESIS\">LACHESIS<\/a>: \u53d1\u8868\u5728NBT\uff0c2017\u5e74\u540e\u4e0d\u518d\u66f4\u65b0<br \/>\n<a href=\"https:\/\/github.com\/marbl\/SALSA\">SALSA<\/a>: \u53d1\u8868\u5728BMC genomics, \u4ecd\u5728\u66f4\u65b0\u4e2d<br \/>\n<a href=\"https:\/\/github.com\/theaidenlab\/3d-dna\">3D-DNA<\/a>: \u53d1\u8868\u5728science\uff0c\u4ecd\u5728\u66f4\u65b0\u4e2d<br \/>\n<a href=\"https:\/\/github.com\/tangerzhang\/ALLHiC\">ALLHiC<\/a>: \u53d1\u8868\u5728Nature Plants, \u7528\u4e8e\u89e3\u51b3\u690d\u7269\u591a\u500d\u4f53\u7ec4\u88c5\u95ee\u9898<\/p>\n<p>\u5bf9\u4e8e\u4e8c\u500d\u4f53\u7269\u79cd\u800c\u8a00\uff0c\u76ee\u524d3D-DNA\u5e94\u8be5\u662f\u7ec4\u88c5\u6548\u679c\u8f83\u597d\u7684\u4e00\u4e2a\u8f6f\u4ef6\u3002<\/p>\n<p>\u8f6f\u4ef6\u5b89\u88c5<br \/>\nLachesis\u6709\u4e24\u4e2a\u4f9d\u8d56\uff1asamtools\uff08\u4f4e\u4e8e0.1.19\u7684\u7248\u672c\uff09\u548cC++\u7684boost\u5e93\uff08\u9700\u8981\u5927\u4e8e1.52.0\u4f46\u662f\u53c8\u4e0d\u80fd\u592a\u9ad8\u6bd4\u59821.67.0\u5c31\u4e0d\u884c\uff09<\/p>\n<pre>curl -o LACHESIS.zip https:\/\/codeload.github.com\/shendurelab\/LACHESIS\/legacy.zip\/master\r\nunzip LACHESIS.zip\r\nmv shendurelab-LACHESIS-2e27abb LACHESIS\r\ncd LACHESIS\r\nexport LACHESIS_BOOST_DIR=\/opt\/biosoft\/boost_1_53_0 #boost_1_64_0\u7248\u672c\u4f7f\u7528\u65f6\u51fa\u73b0\u95ee\u9898\r\nexport LACHESIS_SAMTOOLS_DIR=\/opt\/biosoft\/samtools-0.1.18\r\n.\/configure --with-samtools=\/opt\/biosoft\/samtools-0.1.18 --with-boost=\/opt\/biosoft\/boost_1_53_0\/\r\nmake -j 40\r\nmv src\/bin .\r\nmv src\/Lachesis bin\/<\/pre>\n<p>\u5982\u679cPerl\u7248\u672c\u4e0d\u662f 5.14.2 \uff0c\u9700\u8981\u6253\u5f00bin\u4e0b\u9762\u7684perl\u811a\u672c\uff0c\u5220\u9664\u5982\u4e0b\u4fe1\u606f:<br \/>\n\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/<br \/>\n\/\/ \/\/<br \/>\n\/\/ This software and its documentation are copyright (c) 2014-2015 by Joshua \/\/<br \/>\n\/\/ N. Burton and the University of Washington. All rights are reserved. \/\/<br \/>\n\/\/ \/\/<br \/>\n\/\/ THIS SOFTWARE IS PROVIDED &#8220;AS IS&#8221;, WITHOUT WARRANTY OF ANY KIND, EXPRESS \/\/<br \/>\n\/\/ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF \/\/<br \/>\n\/\/ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. \/\/<br \/>\n\/\/ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY \/\/<br \/>\n\/\/ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT \/\/<br \/>\n\/\/ OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR \/\/<br \/>\n\/\/ THE USE OR OTHER DEALINGS IN THE SOFTWARE. \/\/<br \/>\n\/\/ \/\/<br \/>\n\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/<\/p>\n<p>\u7b2c\u4e00\u884c\u66ff\u6362\u6210#!\/usr\/bin\/perl -w<\/p>\n<p>\u6dfb\u52a0\u73af\u5883\u53d8\u91cf<\/p>\n<pre>echo 'PATH=$PATH:\/opt\/biosoft\/LACHESIS\/bin\/' > ~\/.bashrc<\/pre>\n<p>\u8f6f\u4ef6\u4f7f\u7528<\/p>\n<p>\u5b9e\u9645\u7684\u8f6f\u4ef6\u4f7f\u7528\u8981\u6c42\u4f60\u9700\u8981\u63d0\u4f9b\u81f3\u5c11\u4e24\u7c7b\u8f93\u5165\u6587\u4ef6<br \/>\n\u2022HiC\u6570\u636e\uff0c\u53cc\u7aeffastq\u683c\u5f0f<br \/>\n\u2022\u521d\u59cb\u7ec4\u88c5\uff0cfasta\u683c\u5f0f<\/p>\n<p>\u4f7f\u7528bwa\u6bd4\u5bf9\u5f97\u5230bam\u6587\u4ef6<\/p>\n<pre>samtools faidx draft.asm.fasta\r\nbwa index -a bwtsw draft.asm.fasta\r\nbwa aln -t 155 draft.asm.fasta reads_R1.fastq.gz > reads_R1.sai\r\nbwa aln -t 155 draft.asm.fasta reads_R2.fastq.gz > reads_R2.sai\r\nbwa sampe draft.asm.fasta reads_R1.sai reads_R2.sai reads_R1.fastq.gz reads_R2.fastq.gz > sample.bwa_aln.sam\r\nPreprocessSAMs.pl sample.bwa_aln.sam draft.asm.fasta MBOI\r\nfilterBAM_forHiC.pl sample.bwa_aln.REduced.paired_only.bam sample.clean.sam\r\nsamtools view -bt draft.asm.fasta.fai sample.clean.sam > sample.clean.bam<\/pre>\n<p>\u8bbe\u7f6e\u914d\u7f6e\u6587\u4ef6<\/p>\n<pre>cp \/opt\/biosoft\/LACHESIS\/bin\/INIs\/test_case.ini sample.ini<\/pre>\n<p>SPECIES = test # \u5199\u5b9e\u9645\u7684\u7269\u79cd\u540d\u5373\u53ef<br \/>\nDRAFT_ASSEMBLY_FASTA = draft.asm.fasta # \u5f85\u7ec4\u88c5\u5e8f\u5217\u7684\u5b9e\u9645\u4f4d\u7f6e<br \/>\nSAM_DIR = . #\u8868\u793a\u5f53\u524d\u76ee\u5f55\u4e0b\u67e5\u627e\u6587\u4ef6<br \/>\nSAM_FILES = sample.clean.bam #bam\u6587\u4ef6\u540d<br \/>\nRE_SITE_SEQ = AAGCTT #\u9176\u5207\u8bc6\u522b\u5e8f\u5217<br \/>\nUSE_REFERENCE = 0 #\u4e0d\u4f7f\u7528\u53c2\u8003\u5e8f\u5217<br \/>\nBLAST_FILE_HEAD = . # BLAST\u7684\u8f93\u51fa\u7ed3\u679c<br \/>\nCLUSTER_N = 16 # \u6700\u7ec8\u805a\u7c7b\u6570\u76ee<\/p>\n<p># contig\u4e2d\u6700\u5c0f\u7684\u9176\u5207\u4f4d\u70b9\u6570,<br \/>\nCLUSTER_MIN_RE_SITES=25<br \/>\n# contig\u4e2d\u6700\u5927\u7684link\u5bc6\u5ea6, \u4e5f\u5c31\u662f\u4e00\u4e2a\u533a\u57df\u4e0e\u591a\u4e2acontig\u5b58\u5728\u4fe1\u53f7<br \/>\n# \u53ef\u80fd\u662f\u5f02\u67d3\u8272\u8d28\u6216\u91cd\u590d\u5e8f\u5217<br \/>\nCLUSTER_MAX_LINK_DENSITY=2<br \/>\n# \u5bf9\u4e8eCLUSTER_MIN_RE_SITES\u8fc7\u6ee4\u6389\u7684contig\u5728\u521d\u6b65\u805a\u7c7b\u540e\u8fd8\u6709\u673a\u4f1a\u52a0\u5165\u5df2\u6709\u7684\u5206\u7ec4\u4e2d<br \/>\n# \u5982\u679c\u5b83\u52a0\u5165\u5176\u4e2d\u7684\u4fe1\u53f7\u662f\u52a0\u5165\u53e6\u4e00\u7ec4\u4fe1\u53f7\u76843\u500d<br \/>\nCLUSTER_NONINFORMATIVE_RATIO=3<br \/>\n# \u5141\u8bb8\u6210\u7ec4\u7684\u6700\u5c0f\u9176\u5207\u6570<br \/>\nORDER_MIN_N_RES_IN_TRUNK=15<\/p>\n<p>\u8fd0\u884c:<\/p>\n<pre>ulimit -s 10240\r\nLachesis sample.ini\r\nCreateScaffoldedFasta.pl draft.asm.fasta out\/test_case<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u5728\u7ec4\u88c5\u57fa\u56e0\u7ec4\u65f6\uff0c\u4f7f\u7528\u4e8c\u4ee3\u6216\u4e09\u4ee3\u6570\u636e\u7ec4\u88c5\u5230contigs\u540e\uff0c\u4e0b\u4e00\u6b65\u5c31\u662f\u5c06contig\u63d0\u5347\u5230\u67d3\u8272\u4f53\u6c34\u5e73\u3002\u5982\u679c\u5229\u7528HiC\u6570\u636e\uff0c\u90a3\u4e48\u76ee\u524d\u5e38\u89c1\u7684\u7ec4\u88c5\u8f6f\u4ef6\u6709\u4e0b\u9762\u51e0\u4e2a\uff1a HiRise: 2015\u5e74\u540e\u7684GitHub\u5c31\u4e0d\u518d\u66f4\u65b0 LACHESIS: \u53d1\u8868\u5728NBT\uff0c2017\u5e74\u540e\u4e0d\u518d\u66f4\u65b0 SALSA: \u53d1\u8868\u5728BMC genomics, \u4ecd\u5728\u66f4\u65b0\u4e2d 3D-DNA: \u53d1\u8868\u5728science\uff0c\u4ecd\u5728\u66f4\u65b0\u4e2d ALLHiC: \u53d1\u8868\u5728Nature Plants, \u7528\u4e8e\u89e3\u51b3\u690d\u7269\u591a\u500d\u4f53\u7ec4\u88c5\u95ee\u9898 \u5bf9\u4e8e\u4e8c\u500d\u4f53\u7269\u79cd\u800c\u8a00\uff0c\u76ee\u524d3D-DNA\u5e94\u8be5\u662f\u7ec4\u88c5\u6548\u679c\u8f83\u597d\u7684\u4e00\u4e2a\u8f6f\u4ef6\u3002 \u8f6f\u4ef6\u5b89\u88c5 Lachesis\u6709\u4e24\u4e2a\u4f9d\u8d56\uff1asamtools\uff08\u4f4e\u4e8e0.1.19\u7684\u7248\u672c\uff09\u548cC++\u7684boost\u5e93\uff08\u9700\u8981\u5927\u4e8e1.52.0\u4f46\u662f\u53c8\u4e0d\u80fd\u592a\u9ad8\u6bd4\u59821.67.0\u5c31\u4e0d\u884c\uff09 curl -o LACHESIS.zip https:\/\/codeload.github.com\/shendurelab\/LACHESIS\/legacy.zip\/master unzip LACHESIS.zip mv shendurelab-LACHESIS-2e27abb LACHESIS cd LACHESIS export LACHESIS_BOOST_DIR=\/opt\/biosoft\/boost_1_53_0 #boost_1_64_0\u7248\u672c\u4f7f\u7528\u65f6\u51fa\u73b0\u95ee\u9898 export LACHESIS_SAMTOOLS_DIR=\/opt\/biosoft\/samtools-0.1.18 .\/configure &#8211;with-samtools=\/opt\/biosoft\/samtools-0.1.18 &#8211;with-boost=\/opt\/biosoft\/boost_1_53_0\/ make -j 40 mv src\/bin . mv src\/Lachesis bin\/ \u5982\u679cPerl\u7248\u672c\u4e0d\u662f 5.14.2 \uff0c\u9700\u8981\u6253\u5f00bin\u4e0b\u9762\u7684perl\u811a\u672c\uff0c\u5220\u9664\u5982\u4e0b\u4fe1\u606f: \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ \/\/ \/\/ \/\/ This software [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/491"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=491"}],"version-history":[{"count":3,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/491\/revisions"}],"predecessor-version":[{"id":836,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/491\/revisions\/836"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=491"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=491"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=491"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}