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sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R.
Kuan-Hao Chao1, Kirston Barton2, Sarah Palmer3
1Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.
Genome Biology and Evolution
|February 16, 2021
Summary
sangeranalyseR is a free R package simplifying Sanger sequencing data analysis. It offers flexible processing from read trimming to phylogenetic tree estimation, with interactive reports.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sanger sequencing remains a vital tool for genetic analysis.
- Processing Sanger sequencing data can be complex and time-consuming.
- Existing software may lack comprehensive features or user-friendly interfaces.
Purpose of the Study:
- To introduce sangeranalyseR, a new R package for streamlined Sanger sequencing data analysis.
- To provide a flexible and user-friendly tool for various stages of Sanger data processing.
- To enhance accessibility and efficiency for researchers working with Sanger sequencing data.
Main Methods:
- Developed as a free and open-source R package.
- Offers command-line and interactive Shiny application interfaces.
- Supports ABIF and FASTA input formats.
- Includes functions for read trimming, secondary peak detection, alignment, and phylogenetic analysis.
Main Results:
- sangeranalyseR enables users to process Sanger data from raw reads to aligned contigs efficiently.
- The package provides extensive options for data manipulation and analysis.
- Generates detailed interactive HTML reports and outputs data in FASTA format.
- Includes colorblind-friendly visualization options.
Conclusions:
- sangeranalyseR offers a robust, flexible, and user-friendly solution for Sanger sequencing data analysis.
- Its comprehensive features and accessibility make it a valuable tool for the research community.
- The package facilitates efficient and reproducible analysis of Sanger sequencing data.
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