A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina...

Area of Science:

• Ecology and Conservation Biology
• Bioinformatics and Genomics
• Molecular Ecology

Background:

• Microsatellites are valuable genetic markers for ecological and conservation studies.
• Traditional microsatellite development is costly, time-consuming, and taxa-specific.
• Next-generation sequencing (NGS) offers a faster, cheaper alternative, but bioinformatics tools can be complex for new users.

Purpose of the Study:

• To develop an optimized and user-friendly bioinformatics pipeline for microsatellite marker development from NGS data.
• To streamline the design of microsatellite panels using a graphical user interface.
• To make microsatellite development more accessible to researchers new to bioinformatics.

Main Methods:

• Development of an open-source bioinformatics pipeline integrated into the Galaxy platform.
• Utilized existing software (Trimmomatic, FastQC, Primer3) and novel tools (Pal_finder, PANDAseq, Pal_filter).
• Pipeline processes Illumina paired-end sequences for quality filtering, locus identification, primer design, read assembly, and locus filtering.

Main Results:

• A comprehensive bioinformatics pipeline for microsatellite development was created and packaged within Galaxy.
• The pipeline integrates multiple established and novel programs to automate and optimize marker design.
• A pre-configured Galaxy instance is available, providing a user-friendly graphical interface for the entire process.

Conclusions:

• The developed pipeline significantly optimizes and simplifies microsatellite marker development from NGS data.
• The Galaxy-based platform enhances accessibility and usability for researchers, regardless of their bioinformatics expertise.
• This tool facilitates broader application of microsatellites in ecological and conservation research.