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{"type":"doc","content":[{"type":"heading","attrs":{"id":"bf82b506-23d0-41e4-9d49-e9a20fe5a421","textalign":"inherit","indent":0,"level":1,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"一、前言"}]},{"type":"paragraph","attrs":{"id":"ad57081a-4220-4309-97b6-05aa880c403c","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"在基因组学研究的下半场，精确度与全面性已成为临床诊断和群体研究的核心诉求。然而，单一测序技术始终面临着“鱼与熊掌”的抉择：短读长测序（如 illumina）虽拥有极高的碱基准确性和成本优势，但在应对结构变异（sv）、重复序列及复杂基因组区域时往往力不从心。长读长测序（如 oxford nanopore）凭借超长读长轻松跨越复杂区域，有效识别大型 sv，但其较高的测序成本和在同聚物（homopolymer）区域的 indel 错误率仍是不可忽视的屏障。"}]},{"type":"paragraph","attrs":{"id":"780f4599-9f73-4b4d-9fbf-5a1f9f96bb33","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"传统的混合分析方法往往只是将两种数据独立比对后进行简单的交叉验证，这不仅浪费了长读长数据中蕴含的丰富结构信息，更无法从根本上纠正复杂区域的比对偏移 。此外，长读长高昂的覆盖度要求和巨大的计算开销，让许多实验室望而却步。"}]},{"type":"paragraph","attrs":{"id":"aaf83abc-8049-406e-baca-28b44ed6fdc7","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"rgb(71, 107, 156)","background":""}}],"text":"sentieon 模块化工具箱中的 sentieon-cli dnascope-hybrid 模块，通过创新的算法融合彻底打破僵局。该模块引入了创新的重比对步骤，利用长读长单倍型（haplotype）指导短读长比对。即使在挑战性的医学相关基因（cmrg）和串联重复区域，也能实现近乎完美的变异识别。"}]},{"type":"paragraph","attrs":{"id":"89812a9c-6050-4351-b614-17a875a9af66","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"实测数据表明，"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"rgb(71, 107, 156)","background":""}}],"text":"仅需 5x-10x 的低深度长读长配合标准短读长数据，其 indel 检测准确性即可超越传统 30x 纯长读长流程，变异检测错误率降低 50% 以上。"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"得益于 sentieon 工业级的算法优化，该流程在 x86、arm 等多平台上运行极快，全流程分析耗时约 100 分钟，计算成本最低仅需数美元。"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"rgb(71, 107, 156)","background":""}}],"text":"无论是在精准医疗的临床诊断，还是在大规模的人口基因组计划中，sentieon dnascope hybrid 都为您提供了一个平衡成本、速度与精度的最优解。"}]},{"type":"horizontalrule","attrs":{"id":"1c0c0042-0508-4fbb-8855-0aa370eae7c1","ishoverdraghandle":false}},{"type":"paragraph","attrs":{"id":"5645a441-6dfe-4047-8a03-afcc0cc023c2","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false}},{"type":"heading","attrs":{"id":"806b4403-c511-4402-9131-b0ff21f39acc","textalign":"inherit","indent":0,"level":1,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"二、流程总览"}]},{"type":"paragraph","attrs":{"id":"474f1ea5-c5bd-4410-80e1-73bb15304ea2","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"sentieon® dnascope hybrid是一种利用单一样本的短读长和长读长测序数据结合进行种系变异识别的流程。该流程能够充分发挥两种测序技术的优势，生成的变异识别结果比单独使用短读长或长读长数据更加准确。sentieon-cli通过单条命令完整实现了dnascope hybrid流程。"}]},{"type":"paragraph","attrs":{"id":"fe5b616f-fd34-4d01-81a9-a83e6cf732bc","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"该流程支持以下数据格式作为输入，且短读长和长读长数据均必须提供："}]},{"type":"bulletlist","attrs":{"id":"469c81c4-d26f-4d68-9c29-99705f51c8b7","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"cfc3df38-5930-43e2-bdaf-4f303d597366"},"content":[{"type":"paragraph","attrs":{"id":"d20622b5-be3b-49e0-b430-14c3620fedf5","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"gzip压缩的fastq格式的未比对短读长数据。"}]}]},{"type":"listitem","attrs":{"id":"2c3a7ebb-5b14-457c-9ee0-22454f96b568"},"content":[{"type":"paragraph","attrs":{"id":"1e0640b7-4ff9-4652-8a0a-cb0cd1d4880c","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"bam或cram格式的已比对短读长数据。"}]}]},{"type":"listitem","attrs":{"id":"bf676339-bfb9-427c-bd77-c7e3ce2ded63"},"content":[{"type":"paragraph","attrs":{"id":"9e356094-482f-4bf1-90dc-ad2acee9617b","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"ubam或ucram格式的未比对长读长数据。"}]}]},{"type":"listitem","attrs":{"id":"1d146bf7-61b7-457c-8a91-5c0657876c11"},"content":[{"type":"paragraph","attrs":{"id":"115cf7a3-9446-4465-905a-e595cd1b52a9","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"bam或cram格式的已比对长读长数据。"}]}]}]},{"type":"paragraph","attrs":{"id":"9d07016a-9ec0-4f16-8fa8-e623f9969709","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"流程默认生成以下输出文件："}]},{"type":"bulletlist","attrs":{"id":"99948656-a37d-4dc7-9ac6-a7aeac9d54d9","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"4fa478b7-b05d-45ef-857d-9c323c9806bf"},"content":[{"type":"paragraph","attrs":{"id":"3724cbf7-2dba-4e42-a4fe-aa3a517a902e","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"以vcf格式输出的小变异（单核苷酸变异和插入缺失）。"}]}]},{"type":"listitem","attrs":{"id":"9d2fefbf-e3da-4b90-ad92-6cbfab7a28f8"},"content":[{"type":"paragraph","attrs":{"id":"14378ecb-b8b1-4ca9-9984-5959f2a6ee13","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"以vcf格式输出的结构变异。"}]}]},{"type":"listitem","attrs":{"id":"0ea4af6c-69e2-4621-ae1a-4b14ebaea14b"},"content":[{"type":"paragraph","attrs":{"id":"ed61dc0b-2c1d-43f4-b9fe-d98d804189b3","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"以vcf格式输出的拷贝数变异。"}]}]}]},{"type":"paragraph","attrs":{"id":"52a8a39e-3230-4730-a053-1743b0d90296","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"如果输入是未比对的原始读数，流程还会输出已比对的读数，格式为bam或cram。"}]},{"type":"heading","attrs":{"id":"0b3121a6-7e9e-48ed-9633-41f83f52a96e","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"1.  硬件配置"}]},{"type":"bulletlist","attrs":{"id":"6f91b421-321b-44ba-8a06-010235ff8ccf","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"071d6f21-6077-479b-a4bd-0228b21257cc"},"content":[{"type":"paragraph","attrs":{"id":"0698ed20-3cbf-4d00-a265-cb9f3956bb4d","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"sentieon® 软件包版本 202503.01 或更高。"}]}]},{"type":"listitem","attrs":{"id":"62bc373b-72bc-421d-a66c-fe956e86bd42"},"content":[{"type":"paragraph","attrs":{"id":"a7ddd375-ebd3-4e86-b112-336465cc32d3","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"python 版本 3.11 或更高。"}]}]},{"type":"listitem","attrs":{"id":"0d5e62ff-5bf2-4b68-8c39-cfbaa554d1c8"},"content":[{"type":"paragraph","attrs":{"id":"f8e9e722-9203-4a4c-b7fc-f16b81fa022d","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"bcftools 版本 1.22 或更高。"}]}]},{"type":"listitem","attrs":{"id":"7abc1125-886e-470b-a2c0-24ec97276818"},"content":[{"type":"paragraph","attrs":{"id":"e3f54feb-af0a-4ffc-ac57-a08e99126fc1","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"bedtools。"}]}]},{"type":"listitem","attrs":{"id":"8f18a1f6-17b2-4f76-82ef-6f455ac04f1c"},"content":[{"type":"paragraph","attrs":{"id":"25e0bfc0-c6fa-454f-9589-34259f8cea79","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"multiqc 版本 1.18 或更高，用于生成指标报告。"}]}]},{"type":"listitem","attrs":{"id":"7b9e7e13-acf1-48c3-8e3b-7706b6cf2a74"},"content":[{"type":"paragraph","attrs":{"id":"b9904375-f37a-4623-ae13-2259f9253799","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"samtools 版本 1.16 或更高。"}]}]},{"type":"listitem","attrs":{"id":"10aa7b8d-83d6-415a-a1bc-1e994efd192a"},"content":[{"type":"paragraph","attrs":{"id":"ea469863-fa60-4c34-b25f-85be59fb12d0","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"mosdepth 版本 0.2.6 或更高，用于从长读长数据中收集覆盖度指标。"}]}]}]},{"type":"heading","attrs":{"id":"acd959ea-83bb-410d-8273-4bbf3ef0fd5a","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"2.  基于已比对的短读长与长读长数据的检测胚系变异"}]},{"type":"paragraph","attrs":{"id":"0fdf3ecd-b45d-42d1-92a1-1db86667b3bd","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"只需运行一个命令即可从比对后的短读长序列中检测 snv、indel、sv 和 cnv："}]},{"type":"codeblock","attrs":{"id":"8653b914-8336-4c3f-af27-a097604c0f05","language":"bash","theme":"atom-one-dark","runtimes":0,"ishoverdraghandle":false,"key":"","languagebyai":"shell"},"content":[{"type":"text","text":"sentieon-cli dnascope-hybrid \\\r -r $reference \\\r --sr_aln $srbam \\\r --lr_aln $lrbam \\\r --rgsm rgsm \\\r -m $model_bundle \\\r -t $threads \\\r -g \\\r --skip_multiqc \\\r ${sampleid}.vcf.gz"}]},{"type":"paragraph","attrs":{"id":"4d389cad-ad64-461e-bdbb-0a2936e3aaf1","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"dnascope hybrid 流程需要以下必备参数："}]},{"type":"bulletlist","attrs":{"id":"90f77e39-0258-43db-bc08-0f411297ac3c","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"0ac68cd0-9eb5-4d91-ab4b-c5477d9dba74"},"content":[{"type":"paragraph","attrs":{"id":"35807858-3da6-4c19-9d37-c68b19f72728","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"-r reference"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：参考 fasta 文件的位置。还需要一个参考 fasta 索引文件，即“.fai”文件。"}]}]},{"type":"listitem","attrs":{"id":"2bcd4683-bd96-4971-88f4-f105566eef51"},"content":[{"type":"paragraph","attrs":{"id":"e541fa3d-a3e9-4ad1-b1eb-d0ea3e54da67","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--sr_aln"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：输入的短序列读取数据格式为 bam 或 cram。可以通过在该参数后传递多个文件来提供一个或多个文件。"}]}]},{"type":"listitem","attrs":{"id":"2b7a5b80-1988-4032-a1fe-ca7af6b6c4b2"},"content":[{"type":"paragraph","attrs":{"id":"9c1d1cbe-0231-4ee6-b664-3fed83df06a1","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--lr_aln"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：输入的长读取数据格式为 bam 或 cram。可以通过在该参数后传递多个文件来提供一个或多个文件。"}]}]},{"type":"listitem","attrs":{"id":"cd87009d-f047-4133-8d60-4264b0fe7c04"},"content":[{"type":"paragraph","attrs":{"id":"d9f1dae1-4162-498e-80e5-d159557ee520","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"-m model_bundle"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：模型包的位置。模型包文件位于 sentieon-models 代码库中。"}]}]},{"type":"listitem","attrs":{"id":"26cefe76-aa11-46ba-acfe-56dbc1e804bc"},"content":[{"type":"paragraph","attrs":{"id":"157bdb93-b43d-4206-9e39-a213de7ecaaa","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"sample.vcf.gz"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：snv 和 indel 的输出 vcf 文件的位置。该流程要求输出文件以“.vcf.gz”为后缀。"}]}]}]},{"type":"paragraph","attrs":{"id":"7e3ed66e-4e7b-47ab-b7bc-bfbf8fa11494","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"dnascope hybrid 流程接受以下可选参数："}]},{"type":"bulletlist","attrs":{"id":"fd986b4e-64c8-43dd-8919-f8e9a4f7b568","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"33d01cc2-3c36-45e8-82c2-678667427204"},"content":[{"type":"paragraph","attrs":{"id":"bbfcc943-3de6-473e-b8b5-3e86efa0ed07","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--pop_vcf pop_vcf"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：包含用于 dnamodelapply 的注释信息的群体 vcf 文件的位置。某些模型包文件需要此文件。群体 vcf 文件必须与模型包匹配。"}]}]},{"type":"listitem","attrs":{"id":"f8f79b3b-40bb-44b7-8ef8-3b30d8b9d870"},"content":[{"type":"paragraph","attrs":{"id":"ba0e4dd7-dada-4af3-a4e2-34f244f31a8e","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"-d dbsnp"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：用于标记已知变异的单核苷酸多态性数据库 (dbsnp) 的位置，文件格式为 vcf ("},{"type":"text","marks":[{"type":"code"}],"text":".vcf"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":") 或 bgzip 压缩的 vcf ("},{"type":"text","marks":[{"type":"code"}],"text":".vcf.gz"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":")。仅支持一个文件。提供此文件将使用变异的 dbsnp refsnp id 编号对其进行注释。需要一个 vcf 索引文件。"}]}]},{"type":"listitem","attrs":{"id":"656a8c4f-5503-41e5-8e6b-dd2b9c226285"},"content":[{"type":"paragraph","attrs":{"id":"e26768a6-b560-40e6-80b8-6dab8a7e6d63","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"-b diploid_bed"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：用于限制二倍体变异检测的参考区间，采用 bed 文件格式。提供此文件会将二倍体变异检测限制在 bed 文件内的区间范围内。"}]}]},{"type":"listitem","attrs":{"id":"6dea0a0c-1422-4220-8842-9f54ca7a2595"},"content":[{"type":"paragraph","attrs":{"id":"a9fa8eac-4b8d-4b1a-a956-e127f9509634","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"-t number_threads"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：软件用于运行并行进程的计算线程数。此参数为可选参数；如果省略，则管道将使用服务器拥有的所有线程。"}]}]},{"type":"listitem","attrs":{"id":"550878fd-8c08-45d5-b87d-225f1b0a4c07"},"content":[{"type":"paragraph","attrs":{"id":"1a27d6ef-7c76-449e-a9a7-26d2b8a51b48","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"-g"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：以 gvcf 格式输出变体。该工具将输出一个经过 bgzip 压缩的 gvcf 文件以及相应的索引文件。"}]}]},{"type":"listitem","attrs":{"id":"d7796319-d29b-4c3c-932a-f2a906aab5b1"},"content":[{"type":"paragraph","attrs":{"id":"f04fc550-5363-4dda-a3b7-94b0417581e1","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"-h"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：打印命令行帮助并退出。"}]}]},{"type":"listitem","attrs":{"id":"bee26d60-a14c-4929-9ecd-ae4929f8dced"},"content":[{"type":"paragraph","attrs":{"id":"92e5fb0e-1bfe-470b-a1ee-0f073b1e9385","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--dry_run"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：打印管道命令，但不实际执行它们。"}]}]}]},{"type":"heading","attrs":{"id":"701c4c5b-77a2-4fa9-a130-036d81a1e8bc","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"3.  基于未比对的短读长和长读长数据中检测胚系变异"}]},{"type":"paragraph","attrs":{"id":"8dec55ec-4c9d-4a7d-8e90-264d22fd726c","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"只需运行一个命令即可从未比对的短读长读序列中检测 snv、indel、sv 和 cnv："}]},{"type":"codeblock","attrs":{"id":"b6aa9f7f-9cd5-412d-94e9-4351764c4db8","language":"bash","theme":"atom-one-dark","runtimes":0,"ishoverdraghandle":false,"key":"","languagebyai":"shell"},"content":[{"type":"text","text":"sentieon-cli dnascope-hybrid \\\r -r $reference \\\r --sr_r1_fastq hg002.novaseq.pcr-free.35x.r1.fastq.gz \\\r --sr_r2_fastq hg002.novaseq.pcr-free.35x.r2.fastq.gz\\\r --sr_readgroups \"@rg\\tid:hg002-1\\tsm:hg002\\tlb:hg002-lb-1\\tpl:illumina\"\r --lr_aln $lrbam \\\r --rgsm rgsm \\\r -m $model_bundle \\\r -t $threads \\\r -g \\\r --skip_multiqc \\\r ${sampleid}.vcf.gz"}]},{"type":"paragraph","attrs":{"id":"ecf133cf-b161-4d53-a91f-2940d37cf854","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"dnascope hybrid 流程需要以下参数："}]},{"type":"bulletlist","attrs":{"id":"705c4a44-12a1-449c-a651-a49215a9ebef","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"4cba4228-9448-4a50-8038-eb2fb33e1ad1"},"content":[{"type":"paragraph","attrs":{"id":"30d6d599-b640-4dd7-a2eb-a6474ce0a59a","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--sr_r1_fastq"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：输入的 r1 短读数据为 gzip 压缩的 fastq 格式。可以通过在该参数后传递多个文件来提供一个或多个文件。"}]}]},{"type":"listitem","attrs":{"id":"4ea68f38-f4f9-4b1c-8841-c5a7e85b1a7a"},"content":[{"type":"paragraph","attrs":{"id":"02d8caee-624b-4b2b-a205-46183907a11f","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--sr_r2_fastq"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：输入的 r2 短读数据为 gzip 压缩的 fastq 格式。可以通过在该参数后添加多个文件来提供一个或多个文件。"}]}]},{"type":"listitem","attrs":{"id":"19c2dddd-956e-4746-9e5f-6ec0bfe7c3cc"},"content":[{"type":"paragraph","attrs":{"id":"cf43a2b2-17eb-4c93-b239-58e799b1ce72","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--sr_readgroups"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：每个 fastq 文件的读取组信息。该流程需要相同数量的参数传递给"},{"type":"text","marks":[{"type":"code"}],"text":"--sr_r1_fastq"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"和 "},{"type":"text","marks":[{"type":"code"}],"text":"--sr_readgroups"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"。例如，参数："},{"type":"text","marks":[{"type":"code"}],"text":"--sr_readgroups \"@rg\\tid:hg002-1\\tsm:hg002\\tlb:hg002-lb-1\\tpl:illumina\""}]}]},{"type":"listitem","attrs":{"id":"e564e97b-5031-4d66-b248-cec6b4d4e963"},"content":[{"type":"paragraph","attrs":{"id":"4dee953d-6f4a-4c07-94ce-d4d8e8d9b952","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--lr_aln"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：输入的长读数据，格式为 ubam 或 ucram。可以通过在该参数后传递多个文件来提供一个或多个文件。"}]}]},{"type":"listitem","attrs":{"id":"9c6a7fb7-f904-43c3-9dc8-0a4999be080b"},"content":[{"type":"paragraph","attrs":{"id":"96385892-9a54-4dd5-90eb-d9e1fe860f63","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--lr_align_input"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：指定流程对输入的长读长bam或cram进行比对，如果bam或cram是未比对的。"}]}]}]},{"type":"paragraph","attrs":{"id":"b96abe81-b63c-4b61-b5a8-786c72f731a4","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"dnascope hybrid 流程接受以下可选参数："}]},{"type":"bulletlist","attrs":{"id":"18a9fca8-291b-4ff9-a1c3-de082f30cee7","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"266f3e1a-9fe3-40a4-97ac-636f34294dd7"},"content":[{"type":"paragraph","attrs":{"id":"b83db496-3490-4a97-a045-dfdc1d882971","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--sr_duplicate_marking"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：重复标记设置。markdup 将标记重复的读取序列。rmdup 将删除重复的读取序列。 none 将跳过重复标记。默认设置为 markdup。"}]}]},{"type":"listitem","attrs":{"id":"82ec1514-be22-4a15-b90f-c73d793e8703"},"content":[{"type":"paragraph","attrs":{"id":"8e7ba166-b688-43a6-82f8-340955502927","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--lr_input_ref"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：用于解码输入长读取文件的参考 fasta 文件。长读取 ucram 或 cram 输入时必需。可以与-r参数指定的 fasta 文件不同。"}]}]},{"type":"listitem","attrs":{"id":"38dc9139-9cf2-4280-ab90-1d04e2e75944"},"content":[{"type":"paragraph","attrs":{"id":"d2472b2a-08e9-4243-92fa-7efe33c441dd","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"--bam_format"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：对于输出对齐的文件，请使用 bam 格式而不是 cram 格式。"}]}]}]},{"type":"paragraph","attrs":{"id":"57acc7be-725c-4d5f-904a-6b177ada0d35","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"bold"}],"text":"官方文档："}]},{"type":"bulletlist","attrs":{"id":"f0d7b350-2b46-406b-afc7-7f24c67b39e8","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"05784ff2-7152-48be-8592-118f0a527a13"},"content":[{"type":"paragraph","attrs":{"id":"dfae6579-7e9c-475e-be7b-c742898033d7","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"https://support.sentieon.com/docs/sentieon_cli/#dnascope-hybrid"}]}]}]},{"type":"horizontalrule","attrs":{"id":"10d296ce-2ca2-42f2-9706-4e26ed9ff1ae","ishoverdraghandle":false}},{"type":"paragraph","attrs":{"id":"50d254af-bb83-4d2c-8c32-50a1c283f483","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false}},{"type":"heading","attrs":{"id":"c5e328c8-3ae8-4f68-9b92-6bd15b32d90a","textalign":"inherit","indent":0,"level":1,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"三、流程输出"}]},{"type":"heading","attrs":{"id":"24f8034f-8645-4b8f-b637-2c61087244b1","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"1.  dnascope hybrid 流程输出文件"}]},{"type":"bulletlist","attrs":{"id":"7e1691c6-8fdb-46da-8a6a-875e34570189","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"33ce9200-e658-4a72-bb14-7d2d9ad524a0"},"content":[{"type":"paragraph","attrs":{"id":"ec9ab6d7-98a1-43ae-9b4e-35878c99175b","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"sample.vcf.gz"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：在-b diploid_bed文件所定义的基因组区域内生成的 snv 和 indel 变异检测结果。"}]}]},{"type":"listitem","attrs":{"id":"803ba3e4-64b5-49c1-b4c3-a8e3870cc6ac"},"content":[{"type":"paragraph","attrs":{"id":"7d962ee7-d9e9-4ae1-8540-20930c2607c6","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"sample.sv.vcf.gz"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：来自 sentieon® longreadsv 工具的结构变异检测。"}]}]},{"type":"listitem","attrs":{"id":"ddbf40b3-7c5f-4345-8b43-ffe0c2179936"},"content":[{"type":"paragraph","attrs":{"id":"4330a835-b51d-4ed9-bc22-2ce3ab5c4f6b","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"sample.cnv.vcf.gz"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：来自 sentieon® cnvscope 工具的拷贝数变异检测。"}]}]},{"type":"listitem","attrs":{"id":"a16eb6bd-4c76-445c-8bf5-94cb0fcac380"},"content":[{"type":"paragraph","attrs":{"id":"5bfdcffa-6d1e-43d0-a80e-8826d6fbbe09","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"sample_deduped.cram"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：已对齐、按坐标排序并标记重复项，从输入的 fastq 文件中提取短读数据。"}]}]},{"type":"listitem","attrs":{"id":"048d23ff-b1ea-4cda-b876-ca39e64b53d8"},"content":[{"type":"paragraph","attrs":{"id":"ccb610d3-aac8-4d19-b638-93553b9930a7","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"sample_mm2_sorted_*.cram"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：已比对和坐标排序的长读段，从输入的 ubam、ucram、bam 或 cram 文件中提取数据。"}]}]},{"type":"listitem","attrs":{"id":"5ef3443c-51a7-4419-8df3-05eaf1f01120"},"content":[{"type":"paragraph","attrs":{"id":"ea355660-98d8-4694-a62c-1fd8e261b965","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"code"}],"text":"sample_metrics"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"：包含所分析对象的质量控制指标的目录。"}]}]}]},{"type":"paragraph","attrs":{"id":"e1c6fe8f-7dad-489b-b35f-b07c514c1e09","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"bold"}],"text":"sentieon dnascope hybrid 流程 github 地址："},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"https://github.com/insvast/bioinformatics/tree/main/wgs-dnascope-hybird"}]},{"type":"horizontalrule","attrs":{"id":"f8f06760-b62f-4f32-aa69-e24f0de294dd","ishoverdraghandle":false}},{"type":"paragraph","attrs":{"id":"09dc7ec5-431b-428d-84ed-fa258be2ad09","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false}},{"type":"heading","attrs":{"id":"df1ec749-1856-4b2c-a175-5f092c0947e0","textalign":"inherit","indent":0,"level":1,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"四、实际测试运行"}]},{"type":"heading","attrs":{"id":"5bd650f9-4b16-481c-9c06-a0987f180c45","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"1.  sentieon 软件下载安装"}]},{"type":"bulletlist","attrs":{"id":"13e39ef6-c0d9-4123-987b-cdc4a01f5990","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"1d9fa1f2-20ad-44f6-9230-c4597f60bfe2"},"content":[{"type":"paragraph","attrs":{"id":"6fc7d494-c79c-44c7-9eb1-09ec98ceec72","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"https://ftp.insvast.com/user/sentieon/release/sentieon-genomics-202503.03.tar.gz（适配 x86 架构 cpu 服务器，例如 intel､ amd､ 曙光）"}]}]},{"type":"listitem","attrs":{"id":"94d10c8a-e295-4fff-8abf-cdd9a5d674d3"},"content":[{"type":"paragraph","attrs":{"id":"bc5b6d63-dc7c-474d-9f7d-68958b26598b","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"https://ftp.insvast.com/user/sentieon/release/arm-sentieon-genomics-202503.03.tar.gz（适配 arm 架构 cpu 服务器， 例如华为鲲鹏､ 阿里倚天､ ampere）"}]}]},{"type":"listitem","attrs":{"id":"297687c3-58c4-4783-b9b0-88b3b765b31a"},"content":[{"type":"paragraph","attrs":{"id":"715e3120-2839-42e6-aaa9-59ffe1998b1a","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"软件下载链接需账号与密码，请于后台s信进行获取。"}]}]}]},{"type":"heading","attrs":{"id":"df6f3878-201b-4692-af92-e2a01f593333","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"2.  参考基因组下载"}]},{"type":"codeblock","attrs":{"id":"09552d66-b55c-4af4-a6b8-a5be1929884f","language":"bash","theme":"atom-one-dark","runtimes":0,"ishoverdraghandle":false,"key":"","languagebyai":"bash"},"content":[{"type":"text","text":"# 方法一：\rwget -c https://ftp-trace.ncbi.nlm.nih.gov/referencesamples/giab/release/references/grch38/grch38_giabv3_no_alt_analysis_set_maskedgrc_decoys_map2k3_kmt2c_kcnj18.fasta.gz\r# 方法二：\rcurl -c - -0 --progress-bar https://ftp-trace.ncbi.nlm.nih.gov/referencesamples/giab/release/references/grch38/grch38_giabv3_no_alt_analysis_set_maskedgrc_decoys_map2k3_kmt2c_kcnj18.fasta.gz\r# 解压\rgunzip grch38_giabv3_no_alt_analysis_set_maskedgrc_decoys_map2k3_kmt2c_kcnj18.fasta.gz"}]},{"type":"heading","attrs":{"id":"30b168c5-0b7e-4c9d-9501-2c2474ce30db","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"3.  测试数据下载"}]},{"type":"codeblock","attrs":{"id":"fb53d11e-e9ee-4338-a381-2abbe49a8d54","language":"bash","theme":"atom-one-dark","runtimes":0,"ishoverdraghandle":false,"key":"","languagebyai":"txt"},"content":[{"type":"text","text":"wget -c https://data.nist.gov/od/ds/ark:/88434/mds2-2336/input_fastqs/hg002_35x_pacbio_14kb-15kb.fastq.gz\rwget -c https://data.nist.gov/od/ds/ark:/88434/mds2-2336/input_fastqs/hg002.novaseq.pcr-free.35x.r1.fastq.gz\rwget -c https://data.nist.gov/od/ds/ark:/88434/mds2-2336/input_fastqs/hg002.novaseq.pcr-free.35x.r2.fastq.gz\rwget -c https://42basepairs.com/download/gs/deepvariant/ont-case-study-testdata/hg002_r104_sup_merged.50x.bam"}]},{"type":"paragraph","attrs":{"id":"a347c55d-4dc0-4026-8002-5052749367a2","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"需要注意，giab 早期使用的ont数据为 r9.4.1，对 indel 的检出率较低，而现在一般需要使用 r10.4 版本。"}]},{"type":"heading","attrs":{"id":"3a08678d-547e-4805-a9a8-d09abe53c606","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"4.   分析运行"}]},{"type":"codeblock","attrs":{"id":"ae60e353-b182-4b36-9ef4-5b05e5c7e855","language":"bash","theme":"atom-one-dark","runtimes":0,"ishoverdraghandle":false,"key":"","languagebyai":"bash"},"content":[{"type":"text","text":"sbatch hg002_35x_ill_10x_ont_r104.sh\rsbatch hg002_35x_ill_15x_pb.sh"}]},{"type":"heading","attrs":{"id":"75d38e45-9549-436b-9f4d-9d08e5e982d0","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"5. 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数据：各流程的变异检测准确性统计："}]}]}]},{"type":"image","attrs":{"id":"4f86a3ab-af33-415b-b5ed-05ccf6f2e68e","src":"https://developer.qcloudimg.com/http-save/audit-10646253/98aa9e9505a3acea5dfb745d46373f01.webp","extension":"","align":"center","alt":"","showalt":false,"href":"","boxshadow":"","width":"","aspectratio":0,"status":"success","showtext":true,"ispercentage":false,"percentage":0,"ishoverdraghandle":false}},{"type":"bulletlist","attrs":{"id":"bfd95841-6c9d-4205-8231-b44a5aeb5127","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"85e74f54-7cf2-438d-89e7-d9aba2b1e8db"},"content":[{"type":"paragraph","attrs":{"id":"14d8b371-16cd-49c1-968c-8eb550b40d80","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"illumina+ont 数据：各流程的变异检测准确性统计："}]}]}]},{"type":"image","attrs":{"id":"b0f0a456-6219-4f0a-ad5e-738cc0b668be","src":"https://developer.qcloudimg.com/http-save/audit-10646253/e1d7faae787dd1ec3f23dc04da47114a.webp","extension":"","align":"center","alt":"","showalt":false,"href":"","boxshadow":"","width":"","aspectratio":0,"status":"success","showtext":true,"ispercentage":false,"percentage":0,"ishoverdraghandle":false}},{"type":"paragraph","attrs":{"id":"4391a95b-c62c-45bf-ba81-ee406743bbba","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"dnascope hybrid 的变异识别结果其准确性均高于仅使用短读长或长读长的识别结果，展现出 sentieon dnascope hybrid 混测方法的稳健性与广泛适用性。未来，泛基因组信息也可集成到 ds-hybrid 流程中，从而提供更高的准确性。"}]},{"type":"heading","attrs":{"id":"3ef2a468-10cf-4cbb-a78e-2516fd24df02","textalign":"inherit","indent":0,"level":2,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"7.  耗时统计"}]},{"type":"paragraph","attrs":{"id":"e7d0a0d5-26de-4fcb-b874-7552e47ebdfc","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"本次基准测试环境统一采用 azure standard hb120rs v3 实例（120个vcpu，456 gib 内存，512gb 高级ssd），下表分别展示了在处理illumina+pb数据和illumina+ont数据时，各流程的运行时间与计算成本。"}]},{"type":"paragraph","attrs":{"id":"10bc0ebc-5019-4984-99a0-69e47ba256b9","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"其中，dnascope hybrid流程输出snp/indel/sv/cnv，dnascope longread（长读长）流程输出snp/indel/sv，dnascope（短读长）流程则输出snp/indel/cnv。"}]},{"type":"bulletlist","attrs":{"id":"8526269f-5974-4c7d-89de-ecb219b272ff","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"096baf7b-a41b-4eed-87b2-4e18605f90f6"},"content":[{"type":"paragraph","attrs":{"id":"0b807ebd-3fb9-4254-af5a-afc3a1832f25","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"illumina+pb 数据：计算资源基准结果："}]}]}]},{"type":"image","attrs":{"id":"68e6ebbe-0326-4b56-ac06-3886ba75fd14","src":"https://developer.qcloudimg.com/http-save/audit-10646253/67086ab36d148d2742a391717ba5cbd3.webp","extension":"","align":"center","alt":"","showalt":false,"href":"","boxshadow":"","width":"","aspectratio":0,"status":"success","showtext":true,"ispercentage":false,"percentage":0,"ishoverdraghandle":false}},{"type":"bulletlist","attrs":{"id":"53f28fd2-de5c-4625-a696-84063117080c","ishoverdraghandle":false},"content":[{"type":"listitem","attrs":{"id":"73e4c83c-8e5a-4ae1-8fb9-be007e51a6a7"},"content":[{"type":"paragraph","attrs":{"id":"2ccbdc8a-ac5a-4c20-885a-4f859a38b457","textalign":"inherit","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"illumina+ont 数据：计算资源基准结果："}]}]}]},{"type":"image","attrs":{"id":"64a5dfe5-300f-4e55-87ce-5596b9c99547","src":"https://developer.qcloudimg.com/http-save/audit-10646253/e5b44c02d014fed39161a5ef6bad4c65.webp","extension":"","align":"center","alt":"","showalt":false,"href":"","boxshadow":"","width":"","aspectratio":0,"status":"success","showtext":true,"ispercentage":false,"percentage":0,"ishoverdraghandle":false}},{"type":"horizontalrule","attrs":{"id":"0af70934-bbb1-4718-bb95-3b1636abc49f","ishoverdraghandle":false}},{"type":"heading","attrs":{"id":"53d959cc-3efd-4df7-92d6-aa343bd31b17","textalign":"inherit","indent":0,"level":1,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"五、总结"}]},{"type":"paragraph","attrs":{"id":"eed6671b-f49c-43ae-8a77-c90c8596a916","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"rgb(71, 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吧！"}]},{"type":"horizontalrule","attrs":{"id":"b7f94742-84cf-4898-8f20-9caf42886c99","ishoverdraghandle":false}},{"type":"heading","attrs":{"id":"e31fade5-fd32-4c9d-8471-4b5fd60e26db","textalign":"justify","indent":0,"level":1,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}},{"type":"bold"}],"text":"sentieon软件介绍"}]},{"type":"paragraph","attrs":{"id":"20911348-240a-4ed7-9841-3f58183f82e5","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"sentieon为完整的纯软件基因变异检测二级分析方案，其分析流程完全忠于bwa、gatk、mutect2、star、minimap2、fgbio、picard等金标准的数学模型。在匹配开源流程分析结果的前提下，大幅提升wgs、wes、panel、umi、ctdna、rna等测序数据的分析效率和检出精度，并匹配目前全部第二代、三代测序平台。"}]},{"type":"image","attrs":{"id":"a5663e49-d47a-47dc-9daf-d8454191cbcf","src":"https://developer.qcloudimg.com/http-save/audit-10646253/45c34b88b1aa4cd70f54624b997218e3.webp","extension":"","align":"center","alt":"","showalt":false,"href":"","boxshadow":"","width":"","aspectratio":0,"status":"success","showtext":true,"ispercentage":false,"percentage":0,"ishoverdraghandle":false}},{"type":"paragraph","attrs":{"id":"56158cb1-472b-4fa5-95fc-57268bda783a","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"sentieon软件团队拥有丰富的软件开发及算法优化工程经验，致力于解决生物数据分析中的速度与准确度瓶颈，"},{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"rgb(71, 107, 156)","background":""}},{"type":"bold"}],"text":"为来自于分子诊断、药物研发、临床医疗、人群队列、动植物等多个领域的合作伙伴提供高效精准的软件解决方案，共同推动基因技术的发展。"}]},{"type":"paragraph","attrs":{"id":"ec745633-97ec-44ec-bfc6-19d3af1ffb33","textalign":"justify","indent":0,"color":null,"background":null,"ishoverdraghandle":false},"content":[{"type":"text","marks":[{"type":"textstyle","attrs":{"color":"","background":""}}],"text":"截至2026年4月份，sentieon已经在全球范围内为1860+用户提供服务，用户处理超过7400+pb数据量，被世界一级影响因子刊物如nejm、cell、nature等广泛引用，引用次数超过1900篇。此外，sentieon连续数年摘得了precision fda、dream challenges等多个权威评比的桂冠，在业内获得广泛认可。"}]}]}