{"id":2128,"date":"2014-06-10T01:52:42","date_gmt":"2014-06-09T17:52:42","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2128"},"modified":"2014-06-10T02:16:50","modified_gmt":"2014-06-09T18:16:50","slug":"%e5%a4%9a%e4%b8%aa-genome-assemblies-%e7%9a%84%e6%95%b4%e5%90%88%e7%9a%84%e7%bb%8f%e9%aa%8c","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2128","title":{"rendered":"\u591a\u4e2a genome Assemblies \u7684\u6574\u5408\u7684\u7ecf\u9a8c"},"content":{"rendered":"<p>\u8fdb\u884c\u591a\u4e2a genome Assemblies \u6574\u5408\u7684\u8f6f\u4ef6\u6709\u5f88\u591a\uff1aGAA, GAM, GAM-NGS, GARM, CISA, minimus2, Reconciliator, MAIA \u7b49\u3002<\/p>\n<p>\u6211\u5bf9\u5176\u4e2d\u7684\u4e00\u4e9b\u8fdb\u884c\u4e86\u5c1d\u8bd5\uff0c\u7ed3\u679c\u4e0b\uff1a<\/p>\n<p>1. <strong>GAA<\/strong>\uff1a\u8f6f\u4ef6\u5f88\u5feb\u5c31\u7ed9\u51fa\u4e86\u7ed3\u679c\uff0c\u4f46\u662f\u7ed3\u679c\u660e\u663e\u662f\u9519\u7684\u3002\u6211\u4e0d\u77e5\u9053\u662f\u4e0d\u662f\u7528\u9519\u4e86\uff0c\u4f46\u662f\u8f6f\u4ef6\u8fd0\u884c\u8fc7\u7a0b\u4e2d\u6ca1\u6709\u62a5\u9519\u3002<\/p>\n<p>2. <strong>GAM-NGS<\/strong>\uff1a \u8f6f\u4ef6\u5b89\u88c5\u53ef\u80fd\u4f1a\u51fa\u73b0\u4e00\u4e9b\u95ee\u9898\u3002\u6709\u65f6\u5019\u80fd\u51fa\u7ed3\u679c\uff0c \u5c06 master \u548c slave \u53cd\u8fc7\u6765\u8fd0\u884c\u5374\u4f1a\u6709\u62a5\u9519\u3002\u540c\u65f6\u4f7f\u7528 bowtie2 \u7684\u7ed3\u679c\u4f5c\u4e3a\u8f93\u5165\u4f1a\u62a5\u9519\u3002\u8be5\u7a0b\u5e8f\u5b89\u88c5\u548c\u8fd0\u884c\u592a\u8fc7\u5bb9\u6613\u51fa\u9519\u3002 \u6ca1\u6709\u4f7f\u7528 MUMer \uff0c\u867d\u7136\u8bf4\u662f\u80fd\u8282\u7ea6\u65f6\u95f4\uff0c\u5176\u5b9e\u751f\u6210 sorted \u7684 bam \u6587\u4ef6\u4e5f\u6781\u4e3a\u8017\u65f6\u7684\u3002 \u6700\u540e\uff0c\u5bf9\u4e8e\u6211\u7684\u6570\u636e\uff0c\u8be5\u8f6f\u4ef6\u7684\u6574\u5408\u6548\u679c\u592a\u5dee\u3002<\/p>\n<p>3. <strong>GARM<\/strong>\uff1a\u8f6f\u4ef6\u7684 pipeline \u660e\u663e\u6ca1\u5199\u597d\uff0c\u76f4\u63a5\u62a5\u9519\uff0c\u8fde\u4f7f\u7528\u5176 example data \u90fd\u72c2\u62a5\u9519\u3002 \u4e00\u770b\u4e0b\u8f7d\u7684\u7a0b\u5e8f\u662f\u6570\u5e74\u524d\u7684\uff0c\u4f30\u8ba1\u4f5c\u8005\u4e5f\u6ca1\u4fee\u6539\u5176\u7a0b\u5e8f\u4e86\u3002<\/p>\n<p>4.<strong> Reconciliator<\/strong>\uff1a \u4ece\u5176\u53d1\u8868\u6587\u7ae0\u6240\u8ff0\u7684\u94fe\u63a5\uff0c\u5b8c\u5168\u4e0b\u8f7d\u4e0d\u5230\u8be5\u8f6f\u4ef6\u3002<\/p>\n<p>5. <strong>MAIA<\/strong>\uff1a \u8c8c\u4f3c\u9700\u8981\u4f7f\u7528 matlab\uff0c\u6ca1\u88c5 matlab \u5207\u9700\u8981\u7528\u94b1\u8d2d\u4e70\u7684\u8f6f\u4ef6\uff0c\u8fd9\u4e2a\u5c31\u9ebb\u70e6\u4e86\u3002<\/p>\n<p>6. <strong>minimus2<\/strong>\uff1a \u4f7f\u7528\u8c8c\u4f3c\u9700\u8981\u4e00\u4e9b\u5176\u4ed6\u683c\u5f0f\u7684\u6587\u4ef6\uff0c\u8c8c\u4f3c\u6bd4\u8f83\u9ebb\u70e6\uff0c\u540c\u65f6\u57fa\u56e0\u7ec4\u6574\u5408\u7684\u6548\u679c\u542c\u8bf4\u6bd4\u8f83\u5dee\u3002\u6211\u4e2a\u4eba\u5c31\u4e0d\u53bb\u8d39\u7cbe\u529b\u9a8c\u8bc1\u4e86\u3002<\/p>\n<p>7. <strong>GAM<\/strong>: \u8c8c\u4f3c GAM-NGS \u662f\u5728\u8be5\u8f6f\u4ef6\u57fa\u7840\u4e0a\u505a\u7684\uff0c\u90a3\u4e48\u8fd9\u4e2a\u4f30\u8ba1\u4e5f\u597d\u4e0d\u5230\u54ea\u513f\u53bb\u3002<\/p>\n<p>8. <strong>CISA<\/strong>\uff1a \u8be5\u8f6f\u4ef6\u7ed3\u679c\u8fd8\u4e0d\u9519\uff0c\u4f7f\u7528\u8d77\u6765\u4e5f\u975e\u5e38\u7b80\u5355\u3002\u552f\u4e00\u7684\u7f3a\u70b9\u662f\u8fd0\u7b97\u6781\u5ea6\u8017\u65f6\uff0c\u7279\u522b\u662f\u8fd0\u884c\u7b2c2\u6b65\u7684\u65f6\u5019\uff0c\u5bf9\u4e8e\u8f83\u5927\u7684\u57fa\u56e0\u7ec4\uff0c\u4f7f\u7528\u6b64\u8f6f\u4ef6\u51e0\u4e4e\u662f\u4e0d\u53ef\u80fd\u7684\u4e8b\u60c5\u3002\u63a8\u8350\u4f7f\u7528\u6b64\u8f6f\u4ef6\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u8fdb\u884c\u591a\u4e2a genome Assemblies \u6574\u5408\u7684\u8f6f\u4ef6\u6709\u5f88\u591a\uff1aGAA, GAM &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2128\">\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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2128"}],"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=2128"}],"version-history":[{"count":6,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2128\/revisions"}],"predecessor-version":[{"id":2134,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2128\/revisions\/2134"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2128"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2128"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2128"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}