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Next-generation Sequencing

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Updated: Nov 12, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

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

Hao Chen¹, Yan Lu^1,2, Dongsheng Lu¹

¹Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

BMC Bioinformatics

|March 22, 2021

Summary

Y-LineageTracker is a new bioinformatics tool for analyzing Y-chromosome DNA (Y-DNA) from next-generation sequencing (NGS) data. It accurately determines paternal lineages, haplogroups, and microsatellite variants for evolutionary studies.

Keywords:

NGS NRY haplogroup Population genetics Y-STR Y-chromosome DNA

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Last Updated: Nov 12, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Published on: October 5, 2018

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Published on: June 28, 2018

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

Genetics
Bioinformatics
Population Genetics

Background:

Y-chromosome DNA (Y-DNA) is crucial for tracing paternal lineages.
Next-generation sequencing (NGS) enhances Y-DNA analysis resolution.
Existing computational tools are insufficient for NGS-based Y-DNA studies.

Purpose of the Study:

To develop a comprehensive bioinformatics framework for Y-DNA analysis using NGS data.
To automate the determination of non-recombining region of the Y-chromosome (NRY) haplogroups and Y-STR variants.
To provide robust interpretations for paternal genetics and evolutionary insights.

Main Methods:

Development of Y-LineageTracker, a high-throughput analysis framework.
Integration of NRY haplogroup classification, clustering, phylogeny, and divergence time estimation.
Incorporation of Y-STR genotyping, statistical analysis, network analysis, and TMRCA estimation.

Main Results:

Y-LineageTracker automatically determines NRY haplogroups and Y-STR variants with high resolution.
The tool integrates modules for comprehensive Y-DNA analysis, including paternal genetics and evolution.
Comparative analysis shows Y-LineageTracker outperforms existing tools in performance and visualization.

Conclusions:

Y-LineageTracker is an open-source, user-friendly command-line tool for Y-DNA analysis from NGS data.
It supports both Y-SNP and Y-STR analysis, various input formats, and produces publication-quality figures.
The tool is compatible with Windows, Linux, and macOS, with freely available source code and documentation.