Thomas Krannich, Dimitri Ternovoj, Sofia Paraskevopoulou, Stephan Fuchs
{"title":"CIEVaD:用于快速按需部署基因组变异检测端到端测试的轻量级工作流程集","authors":"Thomas Krannich, Dimitri Ternovoj, Sofia Paraskevopoulou, Stephan Fuchs","doi":"10.3390/v16091444","DOIUrl":null,"url":null,"abstract":"The identification of genomic variants has become a routine task in the age of genome sequencing. In particular, small genomic variants of a single or few nucleotides are routinely investigated for their impact on an organism’s phenotype. Hence, the precise and robust detection of the variants’ exact genomic locations and changes in nucleotide composition is vital in many biological applications. Although a plethora of methods exist for the many key steps of variant detection, thoroughly testing the detection process and evaluating its results is still a cumbersome procedure. In this work, we present a collection of easy-to-apply and highly modifiable workflows to facilitate the generation of synthetic test data, as well as to evaluate the accordance of a user-provided set of variants with the test data. The workflows are implemented in Nextflow and are open-source and freely available on Github under the GPL-3.0 license.","PeriodicalId":501326,"journal":{"name":"Viruses","volume":"114 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"CIEVaD: A Lightweight Workflow Collection for the Rapid and On-Demand Deployment of End-to-End Testing for Genomic Variant Detection\",\"authors\":\"Thomas Krannich, Dimitri Ternovoj, Sofia Paraskevopoulou, Stephan Fuchs\",\"doi\":\"10.3390/v16091444\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The identification of genomic variants has become a routine task in the age of genome sequencing. In particular, small genomic variants of a single or few nucleotides are routinely investigated for their impact on an organism’s phenotype. Hence, the precise and robust detection of the variants’ exact genomic locations and changes in nucleotide composition is vital in many biological applications. Although a plethora of methods exist for the many key steps of variant detection, thoroughly testing the detection process and evaluating its results is still a cumbersome procedure. In this work, we present a collection of easy-to-apply and highly modifiable workflows to facilitate the generation of synthetic test data, as well as to evaluate the accordance of a user-provided set of variants with the test data. The workflows are implemented in Nextflow and are open-source and freely available on Github under the GPL-3.0 license.\",\"PeriodicalId\":501326,\"journal\":{\"name\":\"Viruses\",\"volume\":\"114 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-09-11\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Viruses\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/v16091444\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Viruses","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/v16091444","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
CIEVaD: A Lightweight Workflow Collection for the Rapid and On-Demand Deployment of End-to-End Testing for Genomic Variant Detection
The identification of genomic variants has become a routine task in the age of genome sequencing. In particular, small genomic variants of a single or few nucleotides are routinely investigated for their impact on an organism’s phenotype. Hence, the precise and robust detection of the variants’ exact genomic locations and changes in nucleotide composition is vital in many biological applications. Although a plethora of methods exist for the many key steps of variant detection, thoroughly testing the detection process and evaluating its results is still a cumbersome procedure. In this work, we present a collection of easy-to-apply and highly modifiable workflows to facilitate the generation of synthetic test data, as well as to evaluate the accordance of a user-provided set of variants with the test data. The workflows are implemented in Nextflow and are open-source and freely available on Github under the GPL-3.0 license.