Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data

doi:10.1186/s12859-021-04057-z

	Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
	Chen, Hao 1; Lu, Yan 1,2; Lu, Dongsheng 1; Xu, Shuhua1,3,4,5,6
	2021-03-09
发表期刊	BMC BIOINFORMATICS (IF:2.9[JCR-2023],3.6[5-Year])
ISSN	1471-2105
卷号	22 期号:1
DOI	10.1186/s12859-021-04057-z
摘要	Background: Y-chromosome DNA (Y-DNA) has been used for tracing paternal lineages and offers a clear path from an individual to a known, or likely, direct paternal ancestor. The advance of next-generation sequencing (NGS) technologies increasingly improves the resolution of the non-recombining region of the Y-chromosome (NRY). However, a lack of suitable computer tools prevents the use of NGS data from the Y-DNA studies. Results: We developed Y-LineageTracker, a high-throughput analysis framework that not only utilizes state-of-the-art methodologies to automatically determine NRY haplogroups and identify microsatellite variants of Y-chromosome on a fine scale, but also optimizes comprehensive Y-DNA analysis methods for NGS data. Notably, Y-LineageTracker integrates the NRY haplogroup and Y-STR analysis modules with recognized strategies to robustly suggest an interpretation for paternal genetics and evolution. NRY haplogroup module mainly covers haplogroup classification, clustering analysis, phylogeny construction, and divergence time estimation of NRY haplogroups, and Y-STR module mainly includes Y-STR genotyping, statistical calculation, network analysis, and estimation of time to the most recent common ancestor (TMRCA) based on Y-STR haplotypes. Performance comparison indicated that Y-LineageTracker outperformed existing Y-DNA analysis tools for the high performance and satisfactory visualization effect. Conclusions: Y-LineageTracker is an open-source and user-friendly command-line tool that provide multiple functions to efficiently analyze Y-DNA from NGS data at both Y-SNP and Y-STR level. Additionally, Y-LineageTracker supports various formats of input data and produces high-quality figures suitable for publication. Y-LineageTracker is coded with Python3 and supports Windows, Linux, and macOS platforms, and can be installed manually or via the Python Package Index (PyPI). The source code, examples, and manual of Y-LineageTracker are freely available at or CodeOcean (https://codeocean.com/capsule/7424381/tree).
关键词	Y-chromosome DNA NGS NRY haplogroup Y-STR Population genetics
URL	查看原文
收录类别	SCIE ; EI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000627887200002
出版者	BMC
原始文献类型	Article
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/126162
专题	生命科学与技术学院_特聘教授组_徐书华组
通讯作者	Xu, Shuhua
作者单位	1.Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, Key Lab Computat Biol, Shanghai 200031, Peoples R China; 2.Fudan Univ, Sch Life Sci, Shanghai 200433, Peoples R China; 3.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China; 4.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China; 5.Zhengzhou Univ, Henan Inst Med & Pharmaceut Sci, Zhengzhou 450052, Peoples R China; 6.Fudan Univ, Collaborat Innovat Ctr Genet & Dev, Shanghai 200438, Peoples R China
通讯作者单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Chen, Hao,Lu, Yan,Lu, Dongsheng,et al. Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data[J]. BMC BIOINFORMATICS,2021,22(1).
APA	Chen, Hao,Lu, Yan,Lu, Dongsheng,&Xu, Shuhua.(2021).Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data.BMC BIOINFORMATICS,22(1).
MLA	Chen, Hao,et al."Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data".BMC BIOINFORMATICS 22.1(2021).