ArticleBMC bioinformatics2021
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Trans-Eurasian steppe herder and barley farmer migrations shaped paternal genomic dynamics in Northwest China and Hui evolution.Science advances · 2026Article
- A high-resolution Y-chromosomal panel for forensic paternal lineage tracing and anthropological insight: unraveling the genetic structure of the Dongxiang ethnic minority.International journal of legal medicine · 2026Article
- High-coverage ancient genomes reveal divergent population histories and prehistoric starch-related genetic variation in Japan.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Layers in the sand: The genetic imprint of migration, culture, and Indus craft in the Thar Desert.HGG advances · 2026Article
- Bioarchaeological analysis illustrates the life of a 16th-century Sámi individual from Kitka, Kuusamo, northern Finland.BMC genomics · 2026Article
- Genomic insights into the admixture history and adaptive evolution of the Zhuang people.Molecular biology and evolution · 2026Article
- Genetic and linguistic landscapes of Gansu-Qinghai populations.Fundamental research · 2026Article
- Modern and Ancient Genomes Reveal Neolithic Paternal Expansions of Millet and Rice Farmers and Demic Diffusion from China into Mainland Southeast Asia.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Multiple southward migrations of Neolithic Chinese farmers into Southeast Asia revealed from large-scale Y-chromosome sequences.Science advances · 2026Article
- An ancient Erysipelothrix rhusiopathiae genome recovered from 1400-year-old human remains in the Northern Caucasus.Scientific reports · 2026Article
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- Ancient genomes reveal early-stage admixture and genetic diversity in the Northwestern Kyushu Yayoi.Scientific reports · 2026Article
- YanHuang Paternal Genomic Resource Suggests A Weakly-differentiated Multi-source Admixture in the Formation of Han Founding Ancestral Lineages.Genomics, proteomics & bioinformatics · 2025Article
- Patrilineages of ethnolinguistically diverse populations reveal multifactorial influences on Chinese paternal population stratification.BMC biology · 2025Article
- Introducing the Y-chromosomal Ancestral-like Reference Sequence-Improving the Capture of Human Evolutionary Information.Molecular biology and evolution · 2025Article
- Ancient genomes provide evidence of demographic shift to Slavic-associated groups in Moravia.Genome biology · 2025Article
- Tracing the Genetic Heritage of the Kirgiz People: Dual-Wave Admixture and Ancestry-Biased Adaptation.Molecular biology and evolution · 2025Article
- A draft UAE-based Arab pangenome reference.Nature communications · 2025Article
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Authors and funding
4 authors.
Funding
Abstract
backgroundY-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.
resultsWe 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.
conclusionsY-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 https://www.picb.ac.cn/PGG/resource.php or CodeOcean ( https://codeocean.com/capsule/7424381/tree ).
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