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Updated: Feb 24, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host

Fwu-Shan Shieh^1,2, Patrick Jongeneel¹, Jamin D Steffen¹

¹JBS Science, Inc., Doylestown, Pennsylvania, United States of America.

|August 23, 2017

Summary

This summary is machine-generated.

ChimericSeq is a new software tool that simplifies identifying viral integration sites in host DNA using next-generation sequencing (NGS). This accessible application aids researchers in understanding virus-related diseases and host impacts like cancer.

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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

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Published on: July 27, 2018

Area of Science:

Virology
Bioinformatics
Genomics

Background:

Viral integration site identification is crucial for understanding disease pathogenesis and host impact, such as tumorigenesis.
Next-generation sequencing (NGS) has advanced the study of viral integration but current analysis tools lack broad accessibility.
Analyzing virus-host junction sites in NGS data presents computational challenges for many researchers.

Purpose of the Study:

To develop an accessible software application for identifying and annotating virus-host chimeric reads in NGS data.
To provide a user-friendly tool that overcomes the limitations of current computational methods for viral integration site analysis.
To enhance the understanding of viral integration's role in disease by improving analytical support for the scientific community.

Main Methods:

Development of ChimericSeq, a novel software application with a graphical user interface (GUI).
Ensuring compatibility with both Windows and Mac operating systems for broad accessibility.
Implementation of a pipeline with custom filtering for artifact removal and quantitative analytical reporting.

Main Results:

ChimericSeq is the first software of its kind to offer a GUI for virus-host chimeric read analysis.
The application effectively identifies and annotates viral integration sites within NGS data.
Custom filtering and quantitative reporting provide functional significance to detected integration sites.

Conclusions:

ChimericSeq significantly improves the accessibility of NGS data analysis for viral integration studies.
The user-friendly GUI and cross-platform compatibility expand analytical support to a wider scientific audience.
This tool has the potential to accelerate research into virus-host interactions and associated diseases.