{"id":65468,"date":"2026-09-12T21:57:26","date_gmt":"2026-09-12T13:57:26","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=65468"},"modified":"2026-09-12T21:57:26","modified_gmt":"2026-09-12T13:57:26","slug":"wgs-mitogenome-data-reuse","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/wgs-mitogenome-data-reuse\/","title":{"rendered":"\u5df2\u6709\u5168\u57fa\u56e0\u7ec4\u6570\u636e\uff0c\u8fd8\u80fd\u56de\u7b54\u4ec0\u4e48\u65b0\u95ee\u9898\uff1f\u4e00\u6b21\u7ebf\u7c92\u4f53\u6570\u636e\u590d\u7528\u7814\u7a76\u7684\u542f\u793a"},"content":{"rendered":"

\u4e00\u6279\u5168\u57fa\u56e0\u7ec4\u6d4b\u5e8f\u6570\u636e\u5df2\u7ecf\u5b8c\u6210 SNP \u68c0\u6d4b\u6216\u7fa4\u4f53\u5206\u6790\uff0c\u539f\u59cb FASTQ \u968f\u540e\u8fdb\u5165\u5f52\u6863\u3002\u8fd9\u65f6\uff0c\u5982\u679c\u7814\u7a76\u95ee\u9898\u53d8\u6210\u201c\u6837\u672c\u4e4b\u95f4\u7684\u6bcd\u7cfb\u8c31\u7cfb\u6709\u4ec0\u4e48\u5dee\u5f02\u201d\uff0c\u6216\u8005\u201c\u73b0\u6709\u6807\u8bb0\u662f\u5426\u8db3\u4ee5\u533a\u5206\u6750\u6599\u201d\uff0c\u4e0b\u4e00\u6b65\u672a\u5fc5\u9700\u8981\u7acb\u5373\u91cd\u65b0\u9001\u6837\u3002<\/p>\n

\u66f4\u503c\u5f97\u5148\u505a\u7684\u662f\u6570\u636e\u53ef\u884c\u6027\u8bc4\u4f30\uff1a\u65e7\u6570\u636e\u4e2d\u6709\u6ca1\u6709\u8db3\u591f\u7684\u76ee\u6807\u4fe1\u53f7\uff0c\u80fd\u5426\u5f62\u6210\u53ef\u4fe1\u7684\u65b0\u7ed3\u679c\uff0c\u4ee5\u53ca\u7ee7\u7eed\u5206\u6790\u7684\u6210\u672c\u662f\u5426\u5408\u7406\u3002<\/strong> \u672c\u6587\u4ee5\u4e00\u9879\u86d4\u866b\u7ebf\u7c92\u4f53\u7814\u7a76\u4e3a\u8d77\u70b9\uff0c\u8ba8\u8bba\u53ef\u590d\u7528\u7684\u65b9\u6cd5\uff0c\u7ed9\u51fa\u539f\u521b\u4ee3\u7801\u793a\u4f8b\uff0c\u5e76\u8bf4\u660e\u54ea\u4e9b\u7ed3\u8bba\u9700\u8981\u989d\u5916\u8bc1\u636e\u3002<\/p>\n

\u8fd9\u9879\u7814\u7a76\u63d0\u4f9b\u4e86\u4ec0\u4e48\u8bc1\u636e<\/h2>\n

Woolfe \u7b49\u5728 Scientific Reports<\/em> \u53d1\u8868\u7684\u7814\u7a76\uff0c\u5bf9 149 \u4efd\u86d4\u866b WGS \u6570\u636e\u6bd4\u8f83\u56db\u79cd\u5904\u7406\u8def\u7ebf\uff0c\u518d\u8fdb\u884c\u7ebf\u7c92\u4f53\u7ec4\u88c5\u3002\u6309\u6587\u4e2d\u201c\u5355\u6761 contig \u542b\u5168\u90e8 12 \u4e2a\u86cb\u767d\u7f16\u7801\u57fa\u56e0\u201d\u7684\u53e3\u5f84\uff0c\u7ed3\u679c\u5982\u4e0b\uff1a\u7814\u7a76\u539f\u6587<\/a>\u3002<\/p>\n\n\n\n\n\n\n\n\n
\u5904\u7406\u8def\u7ebf<\/th>\n\u5b8c\u6574\u7ec4\u88c5\u6570<\/th>\n\u5360 149 \u4efd\u8f93\u5165<\/th>\n<\/tr>\n<\/thead>\n
\u76f4\u63a5\u7ec4\u88c5<\/td>\n142<\/td>\n95.3%<\/td>\n<\/tr>\n
Bowtie2 \u53bb\u5bbf\u4e3b<\/td>\n144<\/td>\n96.6%<\/td>\n<\/tr>\n
Deacon \u53bb\u5bbf\u4e3b<\/td>\n146<\/td>\n98.0%<\/td>\n<\/tr>\n
Deacon \u7ebf\u7c92\u4f53\u5e8f\u5217\u5bcc\u96c6<\/td>\n142<\/td>\n95.3%<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

\u8fd9\u4e9b\u767e\u5206\u6bd4\u7531\u539f\u6587\u8ba1\u6570\u6362\u7b97\uff0c\u4e0d\u662f\u901a\u7528\u6210\u529f\u7387<\/strong>\u3002\u7814\u7a76\u8bc6\u522b\u51fa\u65b0\u7684\u7ebf\u7c92\u4f53\u5206\u652f D\uff1b\u4f46\u5e76\u975e 149 \u4efd\u6570\u636e\u90fd\u81ea\u52a8\u5f97\u5230\u65e0\u7f3a\u53e3\u7ed3\u679c\uff0c\u5176\u4e2d\u4e00\u4efd\u7ecf\u8fc7\u4eba\u5de5\u5904\u7406\u4ecd\u6709\u7f3a\u53e3\u3002\u539f\u59cb reads \u56de\u8d34\u68c0\u67e5\u8986\u76d6\u7684\u662f\u5176\u4e2d 30 \u4efd\u3002\u8bba\u6587\u4e5f\u6ca1\u6709\u7ed9\u51fa\u9002\u7528\u4e8e\u5176\u4ed6\u9879\u76ee\u7684\u56fa\u5b9a\u8282\u7701\u6bd4\u4f8b\u3002\u65b9\u6cd5\u4e0e\u7ed3\u679c\u8bf4\u660e<\/a><\/p>\n

\u4ece\u201c\u518d\u51fa\u4e00\u5f20\u56fe\u201d\u8f6c\u5411\u4e00\u4e2a\u660e\u786e\u7684\u65b0\u95ee\u9898<\/h2>\n

\u6570\u636e\u590d\u7528\u7684\u4ef7\u503c\u53d6\u51b3\u4e8e\u5b83\u80fd\u8865\u4e0a\u54ea\u4e00\u6bb5\u8bc1\u636e\u3002\u9488\u5bf9\u5df2\u7ecf\u6301\u6709\u52a8\u7269\u6216\u5bc4\u751f\u866b WGS \u7684\u56e2\u961f\uff0c\u53ef\u4ee5\u5148\u628a\u95ee\u9898\u62c6\u6210\u4ee5\u4e0b\u51e0\u7c7b\uff1b\u8fd9\u662f\u9879\u76ee\u8bbe\u8ba1\u5efa\u8bae\uff0c\u4e0d\u4ee3\u8868\u539f\u8bba\u6587\u9010\u4e00\u9a8c\u8bc1\u4e86\u8fd9\u4e9b\u5e94\u7528\u3002<\/p>\n\n\n\n\n\n\n\n\n\n
\u4f60\u60f3\u56de\u7b54\u7684\u95ee\u9898<\/th>\n\u53ef\u80fd\u589e\u52a0\u7684\u5206\u6790<\/th>\n\u9700\u8981\u540c\u65f6\u5177\u5907\u4ec0\u4e48<\/th>\n<\/tr>\n<\/thead>\n
\u6837\u672c\u662f\u5426\u5b58\u5728\u4e0d\u540c\u6bcd\u7cfb\u8c31\u7cfb\uff1f<\/td>\n\u5019\u9009\u7ebf\u7c92\u4f53\u5e8f\u5217\u3001\u53ef\u9760\u4f4d\u70b9\u6bd4\u5bf9\u4e0e\u7cfb\u7edf\u53d1\u80b2\u5206\u6790<\/td>\n\u8db3\u591f\u76ee\u6807 reads\u3001\u5408\u9002\u53c2\u8003\u548c\u6837\u672c\u6765\u6e90\u8bb0\u5f55<\/td>\n<\/tr>\n
\u6750\u6599\u6807\u7b7e\u6216\u5206\u7ec4\u662f\u5426\u503c\u5f97\u590d\u6838\uff1f<\/td>\n\u5e8f\u5217\u5173\u7cfb\u4e0e\u91c7\u6837\u53f0\u8d26\u4ea4\u53c9\u68c0\u67e5<\/td>\n\u7269\u79cd\u3001\u5730\u70b9\u3001\u5bbf\u4e3b\u6216\u6279\u6b21\u7b49\u5143\u6570\u636e<\/td>\n<\/tr>\n
\u76ee\u524d\u4f7f\u7528\u7684\u5355\u4e2a\u6807\u8bb0\u662f\u5426\u4fe1\u606f\u6709\u9650\uff1f<\/td>\n\u6bd4\u8f83\u5355\u6807\u8bb0\u4e0e\u591a\u57fa\u56e0\u7ed3\u679c\u7684\u4e00\u81f4\u6027<\/td>\n\u53ef\u6bd4\u8f83\u7684\u540c\u6e90\u533a\u57df\u4e0e\u4e00\u81f4\u7684\u8fc7\u6ee4\u53e3\u5f84<\/td>\n<\/tr>\n
\u6838\u57fa\u56e0\u7ec4\u548c\u7ebf\u7c92\u4f53\u4fe1\u53f7\u4e3a\u4f55\u4e0d\u540c\uff1f<\/td>\n\u6838\u4e0e\u7ebf\u7c92\u4f53\u8bc1\u636e\u7684\u8054\u5408\u68c0\u67e5<\/td>\n\u6838\u6570\u636e\u8d28\u91cf\u548c\u53ef\u652f\u6301\u8be5\u95ee\u9898\u7684\u91c7\u6837\u8bbe\u8ba1<\/td>\n<\/tr>\n
\u65e7\u6570\u636e\u503c\u5f97\u7ee7\u7eed\u505a\uff0c\u8fd8\u662f\u9700\u8981\u8865\u5b9e\u9a8c\uff1f<\/td>\n\u4ee3\u8868\u6027\u6837\u672c\u8bd5\u505a\u4e0e\u6210\u672c\u6838\u7b97<\/td>\n\u9884\u5148\u5b9a\u4e49\u7684\u5408\u683c\u6761\u4ef6\u3001\u5de5\u65f6\u548c\u65b0\u589e\u5b9e\u9a8c\u6210\u672c<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

\u8fd9\u4e9b\u5206\u6790\u4e0d\u80fd\u76f4\u63a5\u66ff\u4ee3\u7269\u79cd\u754c\u5b9a\u3001\u771f\u5b9e\u4f20\u64ad\u94fe\u8ffd\u8e2a\u6216\u4e34\u5e8a\u8bca\u65ad\u3002\u4e00\u4e2a\u7ebf\u7c92\u4f53\u805a\u7c7b\u9996\u5148\u8bf4\u660e\u5e8f\u5217\u5173\u7cfb\uff1b\u628a\u5b83\u89e3\u91ca\u4e3a\u5bbf\u4e3b\u95f4\u4f20\u64ad\u3001\u6742\u4ea4\u6216\u72ec\u7acb\u7269\u79cd\uff0c\u8fd8\u9700\u8981\u6838\u57fa\u56e0\u7ec4\u3001\u6d41\u884c\u75c5\u5b66\u6216\u5176\u4ed6\u72ec\u7acb\u8bc1\u636e\u3002<\/p>\n

\u53ef\u590d\u7528\u7684\u6280\u672f\u4eae\u70b9\uff1a\u628a\u6d41\u7a0b\u53d8\u6210\u53ef\u4ee5\u6bd4\u8f83\u7684\u65b9\u6848<\/h2>\n

\u4eae\u70b9\u4e00\uff1a\u5148\u6838\u67e5\u8f93\u5165\uff0c\u907f\u514d\u5bf9\u7740\u7ed3\u679c\u8868\u5bfb\u627e\u5df2\u7ecf\u4e22\u5931\u7684\u5e8f\u5217\u3002<\/strong> MitoZ \u7684\u65b9\u6cd5\u7814\u7a76\u8868\u660e\uff0c\u52a8\u7269\u5168\u57fa\u56e0\u7ec4 shotgun reads \u53ef\u4ee5\u7528\u4e8e\u7ebf\u7c92\u4f53\u7ec4\u88c5\uff0c\u4f46\u516c\u5171\u6570\u636e\u4e5f\u53ef\u80fd\u4e8b\u5148\u79fb\u9664\u4e86\u7ebf\u7c92\u4f53 reads\u3002\u56e0\u6b64\uff0c\u201c\u505a\u8fc7 WGS\u201d\u4e0d\u7b49\u4e8e\u201c\u73b0\u5728\u4ea4\u5230\u624b\u4e0a\u7684\u6587\u4ef6\u4ecd\u4fdd\u7559\u76ee\u6807\u4fe1\u606f\u201d\u3002\u53ea\u6709 SNP \u8868\u6216\u8fc7\u6ee4\u540e\u7684 VCF\uff0c\u901a\u5e38\u4e0d\u80fd\u66ff\u4ee3\u539f\u59cb reads \u5b8c\u6210\u8fd9\u91cc\u8ba8\u8bba\u7684\u7ec4\u88c5\u4efb\u52a1\u3002MitoZ \u65b9\u6cd5\u8bba\u6587<\/a><\/p>\n

\u4eae\u70b9\u4e8c\uff1a\u4fdd\u7559\u76f4\u63a5\u5206\u6790\u7684\u57fa\u7ebf\uff0c\u68c0\u67e5\u989d\u5916\u6b65\u9aa4\u662f\u5426\u771f\u6b63\u6709\u7528\u3002<\/strong> \u53bb\u5bbf\u4e3b\u3001\u76ee\u6807\u5bcc\u96c6\u548c\u53c2\u6570\u8c03\u6574\u90fd\u589e\u52a0\u4e86\u5904\u7406\u73af\u8282\u3002\u53ef\u4ee5\u5bf9\u540c\u4e00\u7ec4\u4ee3\u8868\u6027\u6570\u636e\u6bd4\u8f83\u5019\u9009\u8def\u7ebf\uff0c\u800c\u4e0d\u662f\u5148\u5047\u5b9a\u590d\u6742\u65b9\u6848\u4e00\u5b9a\u66f4\u4f18\u3002\u4f5c\u8005\u516c\u5f00\u4ed3\u5e93\u4e2d\u7684\u9884\u5904\u7406\u3001\u53bb\u5bbf\u4e3b\u3001\u7ec4\u88c5\u4e0e\u7ed8\u56fe\u4ee3\u7801\u53ef\u4ee5\u4f5c\u4e3a\u6d41\u7a0b\u6838\u5bf9\u5165\u53e3\uff1b\u5177\u4f53\u53c2\u6570\u4ecd\u9700\u4e0e\u6b63\u5f0f\u8bba\u6587\u53ca\u8f93\u5165\u8bfb\u957f\u5bf9\u5e94\u3002\u4f5c\u8005\u4ee3\u7801\u4ed3\u5e93<\/a><\/p>\n

\u4eae\u70b9\u4e09\uff1a\u628a\u201c\u7a0b\u5e8f\u5b8c\u6210\u201d\u4e0e\u201c\u7ed3\u679c\u5408\u683c\u201d\u5206\u5f00\u3002<\/strong> \u6211\u4eec\u5efa\u8bae\u81f3\u5c11\u4fdd\u7559\u4ee5\u4e0b\u56db\u5c42\u9a8c\u6536\u8bb0\u5f55\uff1a<\/p>\n

    \n
  1. \u6570\u636e\u5c42\uff1a<\/strong> \u8bfb\u957f\u3001\u8d28\u91cf\u3001\u6709\u6548\u6570\u636e\u91cf\u53ca\u6837\u672c\u6807\u8bc6\u662f\u5426\u53ef\u9760\u3002<\/li>\n
  2. \u5e8f\u5217\u5c42\uff1a<\/strong> \u5019\u9009\u957f\u5ea6\u3001\u672a\u77e5\u78b1\u57fa\u3001\u5f02\u5e38\u91cd\u590d\u548c\u9884\u671f\u57fa\u56e0\u96c6\u5408\u662f\u5426\u5408\u7406\u3002<\/li>\n
  3. \u652f\u6301\u5c42\uff1a<\/strong> reads \u662f\u5426\u8986\u76d6\u5019\u9009\u5e8f\u5217\uff0c\u4f4e\u8986\u76d6\u533a\u57df\u3001\u63a5\u5934\u9644\u8fd1\u548c\u51b2\u7a81\u4f4d\u70b9\u662f\u5426\u9700\u8981\u68c0\u67e5\u3002<\/li>\n
  4. \u89e3\u91ca\u5c42\uff1a<\/strong> \u4e0d\u540c\u5206\u6790\u53e3\u5f84\u662f\u5426\u7ed9\u51fa\u4e00\u81f4\u7ed3\u8bba\uff1b\u5143\u6570\u636e\u662f\u5426\u8db3\u4ee5\u652f\u6301\u751f\u7269\u5b66\u89e3\u91ca\u3002<\/li>\n<\/ol>\n

    \u8fd9\u5957\u9a8c\u6536\u8868\u6bd4\u201c\u67d0\u4e2a\u8f6f\u4ef6\u8fd0\u884c\u6210\u529f\u201d\u66f4\u9002\u5408\u53d8\u6210\u53ef\u4ea4\u4ed8\u7684\u670d\u52a1\u3002\u5b83\u4e5f\u65b9\u4fbf\u628a\u4e0d\u540c\u8def\u7ebf\u7684\u7ed3\u679c\u653e\u5728\u540c\u4e00\u5c3a\u5ea6\u4e0a\u6bd4\u8f83\u3002<\/p>\n

    \u4ee3\u7801\u793a\u4f8b\uff1a\u68c0\u67e5\u4e00\u4e2a\u5df2\u7ecf\u7ec4\u88c5\u51fa\u7684\u5019\u9009\u5e8f\u5217<\/h2>\n

    \u4e0b\u9762\u7ed9\u51fa\u4e00\u6bb5\u72ec\u7acb\u7f16\u5199\u7684 Linux\/Bash \u793a\u4f8b\uff0c\u4f7f\u7528\u53cc\u7aef\u77ed\u8bfb\u957f FASTQ \u548c\u5df2\u7ecf\u5f97\u5230\u7684\u5019\u9009\u7ebf\u7c92\u4f53 FASTA<\/strong>\u3002\u5b83\u5b8c\u6210\u8d28\u63a7\u3001\u56de\u8d34\u548c\u8986\u76d6\u5ea6\u6c47\u603b\uff0c\u4e0d\u5305\u542b\u7ec4\u88c5\u6b65\u9aa4<\/strong>\uff0c\u4e5f\u4e0d\u662f\u539f\u8bba\u6587\u7684\u5b8c\u6574\u590d\u73b0\u3002<\/p>\n

    \u5148\u5c06 mt_depth_summary.py<\/code> \u653e\u5728\u5de5\u4f5c\u76ee\u5f55\uff0c\u51c6\u5907 sample.R1.fq.gz<\/code>\u3001sample.R2.fq.gz<\/code> \u548c candidate.fa<\/code>\u3002\u9700\u8981\u5df2\u5b89\u88c5 fastp\u3001Bowtie2\u3001Python 3\uff0c\u4ee5\u53ca SAMtools 1.13 \u6216\u66f4\u9ad8\u7248\u672c<\/strong>\uff1b\u5b9e\u9645\u9879\u76ee\u5e94\u56fa\u5b9a\u5e76\u8bb0\u5f55\u5177\u4f53\u7248\u672c\u3002\u4e3a\u4e86\u4fbf\u4e8e\u9605\u8bfb\uff0c\u4e0b\u65b9\u5c55\u793a\u4e3b\u8981\u547d\u4ee4\uff1b\u5b8c\u6574\u4ee3\u7801\u5305<\/a>\u4e2d\u7684 check_candidate.sh<\/code> \u53e6\u6709\u8f93\u5165\u548c\u7248\u672c\u68c0\u67e5\u3002<\/p>\n

    set -euo pipefail\n\n# \u4f7f\u7528\u4e00\u4e2a\u4e0d\u5b58\u5728\u7684\u65b0\u76ee\u5f55\uff0c\u907f\u514d\u8986\u76d6\u4e4b\u524d\u7684\u7ed3\u679c\u3002\nout=mt_pilot\nmkdir "$out"\n\nfastp -i sample.R1.fq.gz -I sample.R2.fq.gz \\\n  -o "$out\/clean.R1.fq.gz" -O "$out\/clean.R2.fq.gz" \\\n  --detect_adapter_for_pe --thread 4 \\\n  --html "$out\/fastp.html" --json "$out\/fastp.json"\n\ncp candidate.fa "$out\/candidate.fa"\nsamtools faidx "$out\/candidate.fa"\nbowtie2-build "$out\/candidate.fa" "$out\/mt_index"\n\nbowtie2 --very-sensitive -p 4 -x "$out\/mt_index" \\\n  -1 "$out\/clean.R1.fq.gz" -2 "$out\/clean.R2.fq.gz" \\\n  2>"$out\/map.log" \\\n  | samtools view -u -F 2308 - \\\n  | samtools sort -@ 2 -o "$out\/mapped.bam" -\n\nsamtools index "$out\/mapped.bam"\nsamtools depth -aa -s -q 20 -Q 20 \\\n  "$out\/mapped.bam" >"$out\/depth.tsv"\n\npython3 mt_depth_summary.py \\\n  "$out\/candidate.fa.fai" "$out\/depth.tsv" \\\n  >"$out\/coverage_summary.tsv"\n<\/code><\/pre>\n
    fastp \u7684\u53cc\u7aef\u8f93\u5165\u3001\u63a5\u5934\u68c0\u6d4b\u53ca HTML\/JSON \u62a5\u544a\u53c2\u6570\u53c2\u89c1\u5b98\u65b9\u8bf4\u660e<\/a>\uff1bBowtie2 \u7684 --very-sensitive<\/code> \u662f\u6bd4\u5bf9\u654f\u611f\u6027\u9884\u8bbe\uff0c\u5e76\u4e0d\u610f\u5473\u7740\u7ed3\u679c\u4e00\u5b9a\u771f\u5b9e\u3002Bowtie2 \u624b\u518c<\/a><\/p>\n
    \u8fd9\u91cc\u6709\u51e0\u4e2a\u5f71\u54cd\u7ed3\u679c\u53e3\u5f84\u7684\u7ec6\u8282\uff1a<\/p>\n