Gabriel Renaud, Viviane Slon, Ana T Duggan, Janet Kelso
{"title":"Schmutzi:估计污染和内源性线粒体共识呼吁古代DNA。","authors":"Gabriel Renaud, Viviane Slon, Ana T Duggan, Janet Kelso","doi":"10.1186/s13059-015-0776-0","DOIUrl":null,"url":null,"abstract":"<p><strong>Unlabelled: </strong>Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.</p><p><strong>Availability: </strong>https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"16 ","pages":"224"},"PeriodicalIF":12.3000,"publicationDate":"2015-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-015-0776-0","citationCount":"289","resultStr":"{\"title\":\"Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.\",\"authors\":\"Gabriel Renaud, Viviane Slon, Ana T Duggan, Janet Kelso\",\"doi\":\"10.1186/s13059-015-0776-0\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Unlabelled: </strong>Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.</p><p><strong>Availability: </strong>https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.</p>\",\"PeriodicalId\":48922,\"journal\":{\"name\":\"Genome Biology\",\"volume\":\"16 \",\"pages\":\"224\"},\"PeriodicalIF\":12.3000,\"publicationDate\":\"2015-10-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1186/s13059-015-0776-0\",\"citationCount\":\"289\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s13059-015-0776-0\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-015-0776-0","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.
Unlabelled: Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.
期刊介绍：
Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields.
With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category.
In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
