Intronomics-MIP: a snakemake pipeline for analyzing multilocus intron polymorphisms in species identification and...

Area of Science:

• Genomics
• Bioinformatics
• Molecular Ecology

Background:

• Multi-locus intron polymorphisms (MIPs) are valuable genetic markers for species identification and population studies.
• Existing analysis methods can be complex and time-consuming, hindering broad application.
• Automated pipelines are needed to improve efficiency and reproducibility in analyzing MIPs.

Purpose of the Study:

• To introduce Intronomics-MIP, an automated snakemake-based pipeline for analyzing MIPs.
• To provide a reproducible and scalable tool for processing intron-targeted amplicon sequencing data.
• To demonstrate the pipeline's utility in species delimitation and population structure assessment.

Main Methods:

• The pipeline integrates established bioinformatics tools including Cutadapt, FLASH, and SeekDeep.
• It automates the processing of highly variable intron regions from amplicon sequencing data.
• The snakemake framework ensures reproducibility and facilitates scalability across different datasets and taxa.

Main Results:

• Intronomics-MIP efficiently processes and analyzes multi-locus intron polymorphisms.
• The pipeline demonstrates effectiveness in distinguishing species and assessing population structure, as shown with teleost datasets.
• Performance assessments confirm the pipeline's reliability and scalability.

Conclusions:

• Intronomics-MIP offers an automated, efficient, and reproducible solution for MIP analysis.
• The pipeline supports diverse applications in species identification, cryptic species detection, and population genetics.
• This tool is adaptable to various taxa, advancing molecular ecology research.