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Peak Studio: a tool for the visualization and analysis of fragment analysis files
Jonathan McCafferty1, Robert Reid, Melanie Spencer
1Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.
Environmental Microbiology Reports
|June 14, 2013
Summary
Peak Studio is an open-source software for analyzing molecular fingerprinting data from automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphisms (T-RFLP). It offers rapid visualization and pre-processing for microbial community analysis.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- Molecular fingerprinting techniques like ARISA and T-RFLP are cost-effective for metagenomic analysis.
- Emerging technologies like next-generation sequencing complement established methods.
- Fragment analysis data requires specialized tools for effective visualization and processing.
Purpose of the Study:
- To introduce Peak Studio, a Java-based GUI for analyzing fragment analysis (FSA) files.
- To provide a user-friendly platform for processing ARISA and T-RFLP data.
- To facilitate downstream statistical analysis of microbial community structures.
Main Methods:
- Developed a Java-based graphical user interface (GUI) named Peak Studio.
- Integrated a peak-calling algorithm with adjustable parameters.
- Enabled immediate visualization of parameter adjustments and downstream principal component analysis (PCA) clustering.
- Ensured cross-platform compatibility (Windows, OS X, Linux).
Main Results:
- Peak Studio allows interactive adjustment of peak-calling parameters.
- Users can visualize the impact of parameter changes on PCA clustering in real-time.
- The software supports saving data in multiple formats for further analysis.
- Open-source nature allows free deployment and modification.
Conclusions:
- Peak Studio offers a flexible and accessible solution for processing ARISA and T-RFLP data.
- The software streamlines pre-processing, enhancing the efficiency of microbial community analysis.
- It serves as a valuable tool for researchers utilizing molecular fingerprinting techniques.
