{"id":66339,"date":"2026-11-04T09:09:34","date_gmt":"2026-11-04T01:09:34","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66339"},"modified":"2026-11-04T09:09:34","modified_gmt":"2026-11-04T01:09:34","slug":"nanots-long-read-rna-snp-server-memory","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/nanots-long-read-rna-snp-server-memory\/","title":{"rendered":"\u9ed8\u8ba4\u53c2\u6570\u5403\u6389126 GB\u5185\u5b58\uff1aNanoTS\u957f\u8bfb\u957f\u8f6c\u5f55\u7ec4SNP\u5206\u6790\uff0c\u4e3a\u4ec0\u4e48\u66f4\u9002\u5408\u653e\u5230\u670d\u52a1\u5668\u4e0a\uff1f"},"content":{"rendered":"
\n

\u957f\u8bfb\u957f\u8f6c\u5f55\u7ec4\u4e0d\u53ea\u56de\u7b54\u201c\u8868\u8fbe\u4e86\u591a\u5c11\u201d\uff0c\u8fd8\u53ef\u80fd\u540c\u65f6\u770b\u89c1\u5b8c\u6574\u8f6c\u5f55\u672c\u3001\u7b49\u4f4d\u57fa\u56e0\u8868\u8fbe\u548c\u8f6c\u5f55\u672c\u4e2d\u7684\u5355\u6838\u82f7\u9178\u53d8\u5f02\u3002\u4f46\u771f\u6b63\u628aONT cDNA\u6216direct RNA\u7684BAM\u4ea4\u7ed9\u53d8\u5f02\u68c0\u6d4b\u5de5\u5177\u540e\uff0c\u5f88\u591a\u56e2\u961f\u624d\u53d1\u73b0\uff1a\u96be\u70b9\u4e0d\u53ea\u662f\u7b97\u6cd5\uff0c\u800c\u662f\u8986\u76d6\u5ea6\u6781\u4e0d\u5747\u5300\u3001\u5019\u9009\u4f4d\u70b9\u6570\u91cf\u5de8\u5927\u3001\u5206\u76f8\u9700\u8981\u53cd\u590d\u8bfb\u5199BAM\uff0c\u4ee5\u53ca\u5185\u5b58\u5cf0\u503c\u96be\u4ee5\u51ed\u6587\u4ef6\u5927\u5c0f\u9884\u4f30\u3002<\/p>\n

2026\u5e74\u53d1\u8868\u4e8e\u300aNature Methods\u300b\u7684NanoTS\uff0c\u6b63\u662f\u4e3a\u957f\u8bfb\u957f\u8f6c\u5f55\u7ec4SNP\u68c0\u6d4b\u8bbe\u8ba1\u7684\u6df1\u5ea6\u5b66\u4e60\u5de5\u5177\u3002\u8bba\u6587\u62a5\u544a\uff0c\u5728\u81f3\u5c115\u6761\u66ff\u4ee3\u7b49\u4f4d\u57fa\u56e0\u652f\u6301\u7684\u4f4d\u70b9\u4e0a\uff0cNanoTS\u5728direct RNA\u548ccDNA\u6570\u636e\u4e2d\u7684F1\u5206\u522b\u8d85\u8fc70.980\u548c0.966\uff1b\u4f46\u5b98\u65b9\u4ed3\u5e93\u540c\u65f6\u7ed9\u51fa\u4e00\u4e2a\u5f88\u6709\u73b0\u5b9e\u610f\u4e49\u7684\u8d44\u6e90\u6570\u5b57\uff1a\u5168\u8f6c\u5f55\u7ec4ONT cDNA\u6570\u636e\u6309\u9ed8\u8ba4\u53c2\u6570\u8fd0\u884c\uff0c\u5cf0\u503c\u5185\u5b58\u7ea6126 GB\u3001\u8017\u65f6\u7ea621\u5c0f\u65f6\u3002\u4e5f\u5c31\u662f\u8bf4\uff0c\u4e00\u53f0\u5e38\u89c1\u768432 GB\u621664 GB\u5de5\u4f5c\u7ad9\uff0c\u5373\u4f7fCPU\u8fd8\u7a7a\u95f2\uff0c\u4e5f\u53ef\u80fd\u5148\u88ab\u5185\u5b58\u5361\u4f4f\u3002<\/p>\n

\"NanoTS\u957f\u8bfb\u957f\u8f6c\u5f55\u7ec4SNP\u5206\u6790\u7b97\u529b\u89c4\u5212\u6d77\u62a5\"
NanoTS\u8d44\u6e90\u89c4\u5212\uff1a\u5019\u9009\u9608\u503c\u65e2\u5f71\u54cd\u5185\u5b58\u548c\u65f6\u95f4\uff0c\u4e5f\u5f71\u54cd\u4f4e\u652f\u6301\u4f4d\u70b9\u7684\u4fdd\u7559\u8303\u56f4\u3002<\/figcaption><\/figure>\n

NanoTS\u89e3\u51b3\u7684\u4e0d\u662f\u666e\u901aDNA\u53d8\u5f02\u68c0\u6d4b<\/h2>\n

RNA\u6570\u636e\u7684\u8986\u76d6\u968f\u57fa\u56e0\u8868\u8fbe\u91cf\u5267\u70c8\u53d8\u5316\uff0c\u540c\u4e00\u4f4d\u70b9\u8fd8\u4f1a\u53d7\u5230\u526a\u63a5\u5f02\u6784\u4f53\u3001\u7b49\u4f4d\u57fa\u56e0\u7279\u5f02\u8868\u8fbe\u3001\u94fe\u504f\u501a\u548cread\u7aef\u90e8\u9519\u8bef\u5f71\u54cd\u3002NanoTS\u5148\u7528\u672a\u5206\u76f8\u6a21\u578b\u4ea7\u751f\u9ad8\u7f6e\u4fe1SNP\uff0c\u518d\u501f\u52a9WhatsHap\u628areads\u62c6\u4e3a\u4e24\u4e2a\u5355\u500d\u578b\uff0c\u6700\u540e\u7528\u5206\u76f8\u6a21\u578b\u91cd\u65b0\u5224\u522b\u3002\u6a21\u578b\u5c06\u5019\u9009\u4f4d\u70b9\u4e0a\u4e0b\u6e38\u78b1\u57fa\u6bd4\u4f8b\u3001\u78b1\u57fa\u71b5\u3001\u8986\u76d6\u5ea6\u3001\u8dddread\u672b\u7aef\u8ddd\u79bb\u4ee5\u53ca\u90bb\u8fd1\u5019\u9009SNP\u7b49\u7279\u5f81\u4e00\u8d77\u8f93\u5165\u5377\u79ef\u7f51\u7edc\u548c\u5168\u8fde\u63a5\u5c42\u3002\u8bba\u6587\u7ed9\u51fa\u7684\u672a\u5206\u76f8\u3001\u5206\u76f8\u6a21\u578b\u53c2\u6570\u91cf\u5206\u522b\u4e3a170,455\u548c219,735\uff0c\u6a21\u578b\u672c\u8eab\u5e76\u4e0d\u7b97\u5927\uff0c\u771f\u6b63\u5360\u8d44\u6e90\u7684\u662f\u5927\u89c4\u6a21\u5019\u9009\u4f4d\u70b9\u7684\u7279\u5f81\u63d0\u53d6\u3001BAM\u626b\u63cf\u548c\u4e2d\u95f4\u7ed3\u679c\u3002<\/p>\n

\u4e00\u5f20\u8868\u770b\u61c2\u8d44\u6e90\u4e3a\u4ec0\u4e48\u4f1a\u7a81\u7136\u653e\u5927<\/h2>\n
\n\n\n\n\n\n\n\n\n
\u573a\u666f<\/th>\n\u5b98\u65b9\u62a5\u544a\u5cf0\u503c\u5185\u5b58<\/th>\n\u5b98\u65b9\u62a5\u544a\u8017\u65f6<\/th>\n\u8d44\u6e90\u5224\u65ad<\/th>\n<\/tr>\n<\/thead>\n
ONT cDNA\uff0c\u5168\u8f6c\u5f55\u7ec4\uff0c\u9ed8\u8ba4\u9608\u503c<\/td>\n\u7ea6126 GB<\/td>\n\u7ea621\u5c0f\u65f6<\/td>\n\u5efa\u8bae\u81f3\u5c11160 GB\u5185\u5b58\u5e76\u9884\u7559\u7cfb\u7edf\u7a7a\u95f4<\/td>\n<\/tr>\n
ONT cDNA\uff0c--ALT 5<\/code><\/td>\n\u7ea621 GB<\/td>\n\u7ea68\u5c0f\u65f6<\/td>\n\u53ef\u663e\u8457\u964d\u8f7d\uff0c\u4f46\u4f1a\u6539\u53d8\u4f4e\u652f\u6301\u4f4d\u70b9\u7684\u7eb3\u5165\u8303\u56f4<\/td>\n<\/tr>\n
ONT direct RNA\uff0c\u9ed8\u8ba4\u9608\u503c<\/td>\n\u7ea614 GB<\/td>\n\u7ea66\u5c0f\u65f6<\/td>\n\u5355\u6837\u672c\u538b\u529b\u8f83\u5c0f\uff0c\u591a\u6837\u672c\u5e76\u53d1\u4ecd\u9700\u89c4\u5212<\/td>\n<\/tr>\n
ONT direct RNA\uff0c--ALT 5<\/code><\/td>\n\u7ea67 GB<\/td>\n\u7ea65\u5c0f\u65f6<\/td>\n\u9002\u5408\u9884\u8dd1\u4e0e\u6d41\u7a0b\u9a8c\u8bc1\uff0c\u4e0d\u7b49\u4e8e\u9002\u5408\u6240\u6709\u7814\u7a76\u76ee\u6807<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u8fd9\u4e9b\u6570\u5b57\u6765\u81eaNanoTS\u5b98\u65b9\u4ed3\u5e93\u7684\u7814\u7a76\u6570\u636e\uff0c\u4e0d\u662f\u4efb\u4f55\u6837\u672c\u7684\u56fa\u5b9a\u627f\u8bfa\u3002\u5b9e\u9645\u8d44\u6e90\u8fd8\u4f1a\u53d7BAM\u4f53\u79ef\u3001\u8868\u8fbe\u6df1\u5ea6\u3001\u53c2\u8003\u7248\u672c\u3001\u5019\u9009\u4f4d\u70b9\u6570\u3001\u7ebf\u7a0b\u6570\u548c\u5b58\u50a8\u901f\u5ea6\u5f71\u54cd\u3002\u66f4\u91cd\u8981\u7684\u662f\uff0c\u628a--ALT<\/code>\u4ece\u9ed8\u8ba42\u63d0\u9ad8\u52305\u867d\u7136\u80fd\u8ba9cDNA\u5185\u5b58\u4ece\u7ea6126 GB\u964d\u5230\u7ea621 GB\uff0c\u5374\u53ef\u80fd\u8fc7\u6ee4\u771f\u5b9e\u7684\u4f4e\u8868\u8fbe\u3001\u7b49\u4f4d\u57fa\u56e0\u5931\u8861\u6216\u7a00\u6709\u8f6c\u5f55\u672c\u4f4d\u70b9\u3002\u8d44\u6e90\u4f18\u5316\u4e0d\u80fd\u53ea\u770b\u201c\u80fd\u4e0d\u80fd\u8dd1\u5b8c\u201d\uff0c\u8fd8\u8981\u56de\u7b54\u201c\u5220\u6389\u7684\u5019\u9009\u662f\u5426\u4f1a\u5f71\u54cd\u751f\u7269\u5b66\u95ee\u9898\u201d\u3002<\/p>\n

\u53ef\u590d\u73b0\u7684\u670d\u52a1\u5668\u6d41\u7a0b\uff1a\u5148\u5c0f\u533a\u57df\uff0c\u518d\u5168\u6837\u672c<\/h2>\n

NanoTS\u76ee\u524d\u4ec5\u652f\u6301Linux\uff0c\u5b98\u65b9\u63d0\u4f9bConda\u548cSingularity\u3002\u6a21\u578b\u8981\u4e0e\u5e73\u53f0\u3001\u6587\u5e93\u548c\u5316\u5b66\u7248\u672c\u4e25\u683c\u5339\u914d\uff1aONT cDNA\u3001ONT direct RNA\u4e0ePacBio MAS-seq\u4e0d\u80fd\u6df7\u7528\u3002\u6b63\u5f0f\u8ba1\u7b97\u524d\uff0c\u5148\u786e\u8ba4BAM\u5df2\u7ecf\u6309\u5750\u6807\u6392\u5e8f\u5e76\u5efa\u7acb\u7d22\u5f15\uff0c\u53c2\u8003\u57fa\u56e0\u7ec4\u4e0e\u6bd4\u5bf9\u65f6\u4f7f\u7528\u7684\u7248\u672c\u4e00\u81f4\u3002<\/p>\n

git clone https:\/\/github.com\/Xinglab\/NanoTS.git\r\ncd NanoTS\r\nconda env create -f environment.yml\r\nconda activate nanoTS\r\npip install .\r\n\r\n# \u5148\u5728\u76ee\u6807\u67d3\u8272\u4f53\u6216\u5c0f\u533a\u57df\u9a8c\u8bc1\u6a21\u578b\u3001\u53c2\u8003\u548c\u8f93\u51fa\r\nnanoTS full_pipeline \\\r\n  --bam sample.sorted.bam \\\r\n  --ref GRCh38.fa \\\r\n  --model_unphased models\/unphased_cDNA_nanopore_R104_HG002.pth \\\r\n  --model_phased models\/phased_cDNA_nanopore_R104_HG002.pth \\\r\n  --outdir nanots_chr22 \\\r\n  --region chr22 --threads 24 --ALT 5\r\n<\/code><\/pre>\n
\u5c0f\u533a\u57df\u8dd1\u901a\u540e\uff0c\u518d\u6839\u636e\u5019\u9009\u4f4d\u70b9\u6570\u91cf\u51b3\u5b9a\u662f\u5426\u6062\u590d\u9ed8\u8ba4--ALT 2<\/code>\u3002\u5efa\u8bae\u540c\u65f6\u8bb0\u5f55\/usr\/bin\/time -v<\/code>\u7684\u6700\u5927\u5e38\u9a7b\u5185\u5b58\u3001\u5899\u949f\u65f6\u95f4\u548c\u9000\u51fa\u72b6\u6001\uff0c\u5e76\u4fdd\u7559\u8f6f\u4ef6\u7248\u672c\u3001\u6a21\u578b\u6587\u4ef6\u6821\u9a8c\u503c\u3001\u53c2\u8003FASTA\u53ca\u7d22\u5f15\u3002\u6279\u91cf\u6837\u672c\u4e0d\u8981\u7b80\u5355\u540c\u65f6\u542f\u52a8\uff1a\u4e24\u4e2a\u9ed8\u8ba4cDNA\u4efb\u52a1\u7406\u8bba\u4e0a\u5c31\u53ef\u80fd\u4e89\u7528250 GB\u4ee5\u4e0a\u5185\u5b58\uff1b\u66f4\u7a33\u59a5\u7684\u505a\u6cd5\u662f\u7528\u8c03\u5ea6\u5668\u9650\u5236\u5e76\u53d1\uff0c\u628aBAM\u548c\u4e34\u65f6\u76ee\u5f55\u653e\u5728\u672c\u5730NVMe\u5de5\u4f5c\u76d8\uff0c\u7ed3\u675f\u540e\u518d\u628aVCF\u3001\u65e5\u5fd7\u548c\u5fc5\u8981\u4e2d\u95f4\u6587\u4ef6\u5f52\u6863\u5230\u5bb9\u91cf\u76d8\u3002<\/p>\n
\u522b\u6309BAM\u5927\u5c0f\u76f4\u63a5\u4e70\u5185\u5b58\uff1a\u5148\u505a\u4e00\u6b21\u8d44\u6e90\u753b\u50cf<\/h2>\n
\u540c\u6837\u662f100 GB\u7684BAM\uff0c\u5019\u9009\u4f4d\u70b9\u6570\u91cf\u53ef\u80fd\u56e0\u4e3a\u6d4b\u5e8f\u6df1\u5ea6\u3001\u7ec4\u7ec7\u8868\u8fbe\u8c31\u548c\u8fc7\u6ee4\u9608\u503c\u800c\u76f8\u5dee\u5f88\u5927\uff0c\u5185\u5b58\u5cf0\u503c\u4e5f\u4e0d\u4f1a\u7ebf\u6027\u4e00\u81f4\u3002\u670d\u52a1\u5668\u89c4\u5212\u5e94\u5148\u4ece\u4e00\u4e2a\u4ee3\u8868\u6027\u6837\u672c\u62bd\u53d6chr22\u6216\u82e5\u5e72\u76ee\u6807\u57fa\u56e0\u533a\u95f4\uff0c\u5206\u522b\u4ee5--ALT 2<\/code>\u548c--ALT 5<\/code>\u8bd5\u8dd1\uff0c\u8bb0\u5f55\u5019\u9009\u4f4d\u70b9\u6570\u3001\u5cf0\u503c\u5185\u5b58\u3001CPU\u5229\u7528\u7387\u548c\u4e34\u65f6\u76ee\u5f55\u589e\u91cf\u3002\u82e5\u5185\u5b58\u968f\u5019\u9009\u4f4d\u70b9\u5feb\u901f\u589e\u957f\uff0c\u5c31\u4f18\u5148\u4f7f\u7528\u5927\u5185\u5b58\u8282\u70b9\uff1b\u82e5CPU\u5229\u7528\u7387\u4e0d\u9ad8\u800cI\/O\u7b49\u5f85\u660e\u663e\uff0c\u5219\u5e94\u5148\u6539\u5584NVMe\u5de5\u4f5c\u76d8\u548cBAM\u7d22\u5f15\uff0c\u800c\u4e0d\u662f\u76f2\u76ee\u589e\u52a0\u6838\u5fc3\u6570\u3002<\/p>\n
\u6279\u91cf\u5206\u6790\u8fd8\u8981\u4e3a\u5931\u8d25\u91cd\u8dd1\u7559\u4f59\u91cf\u3002\u63a8\u8350\u628a\u6bcf\u4e2a\u6837\u672c\u62c6\u6210\u72ec\u7acb\u4efb\u52a1\uff0c\u7533\u8bf7\u5185\u5b58\u65f6\u6309\u5b9e\u6d4b\u5cf0\u503c\u518d\u755920%\u81f330%\u7f13\u51b2\uff0c\u5e76\u8bbe\u7f6e\u8c03\u5ea6\u5668\u7684\u5185\u5b58\u4e0a\u9650\u548c\u8d85\u65f6\u63d0\u9192\u3002\u8f93\u5165BAM\u53ea\u8bfb\uff0c\u8f93\u51fa\u76ee\u5f55\u6309\u6837\u672c\u9694\u79bb\uff0c\u65e5\u5fd7\u4e2d\u5199\u5165\u547d\u4ee4\u3001\u5f00\u59cb\u65f6\u95f4\u3001\u7ed3\u675f\u65f6\u95f4\u3001\u4e3b\u673a\u548c\u8f6f\u4ef6\u7248\u672c\u3002\u8fd9\u6837\u5373\u4f7f\u5355\u4e2a\u6837\u672c\u56e0\u5185\u5b58\u4e0d\u8db3\u9000\u51fa\uff0c\u4e5f\u4e0d\u4f1a\u62d6\u57ae\u6574\u53f0\u670d\u52a1\u5668\u6216\u6c61\u67d3\u5176\u4ed6\u7ed3\u679c\u3002\u5bf9\u4e8e\u5341\u51e0\u4e2a\u4ee5\u4e0a\u6837\u672c\uff0c\u53ef\u5148\u5b8c\u6210\u4f4e\u98ce\u9669\u7684\u5c0f\u533a\u57df\u9884\u8dd1\uff0c\u518d\u5206\u6279\u653e\u5927\u5168\u8f6c\u5f55\u7ec4\uff0c\u907f\u514d\u4e00\u6b21\u6027\u6392\u961f\u540e\u624d\u53d1\u73b0\u6a21\u578b\u9009\u9519\u6216\u53c2\u8003\u4e0d\u4e00\u81f4\u3002<\/p>\n
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\u8d44\u6599\u6765\u6e90\uff1a<\/strong> Nature Methods\u8bba\u6587<\/a>\uff1bNanoTS\u5b98\u65b9GitHub<\/a>\u3002<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"
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