READv2：考古基因组学中生物相关性的高级和用户友好检测

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-08-12 DOI:10.1186/s13059-024-03350-3

Erkin Alaçamlı, Thijessen Naidoo, Merve N. Güler, Ekin Sağlıcan, Şevval Aktürk, Igor Mapelli, Kıvılcım Başak Vural, Mehmet Somel, Helena Malmström, Torsten Günther

{"title":"READv2：考古基因组学中生物相关性的高级和用户友好检测","authors":"Erkin Alaçamlı, Thijessen Naidoo, Merve N. Güler, Ekin Sağlıcan, Şevval Aktürk, Igor Mapelli, Kıvılcım Başak Vural, Mehmet Somel, Helena Malmström, Torsten Günther","doi":"10.1186/s13059-024-03350-3","DOIUrl":null,"url":null,"abstract":"The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"84 1","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics\",\"authors\":\"Erkin Alaçamlı, Thijessen Naidoo, Merve N. Güler, Ekin Sağlıcan, Şevval Aktürk, Igor Mapelli, Kıvılcım Başak Vural, Mehmet Somel, Helena Malmström, Torsten Günther\",\"doi\":\"10.1186/s13059-024-03350-3\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.\",\"PeriodicalId\":12611,\"journal\":{\"name\":\"Genome Biology\",\"volume\":\"84 1\",\"pages\":\"\"},\"PeriodicalIF\":10.1000,\"publicationDate\":\"2024-08-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genome Biology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s13059-024-03350-3\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-024-03350-3","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

全基因组古 DNA 分析的出现彻底改变了我们对史前社会的认识。然而，由于分析古 DNA 所面临的挑战，研究这些群体的生物亲缘关系需要量身定制的方法。READv2 是最广泛使用的工具在 Python3 上的优化实现，它在速度和准确性上都超越了前者，从而解决了这些难题。在数据量足够大的情况下，它可以对三等亲缘关系进行分类，并区分两类一等亲缘关系（全同胞和亲子）。READv2 可以对生物亲缘关系进行用户友好、高效和细致的分析，从而促进对过去社会结构的深入了解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics

The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.