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

## TL;DR

Intronomics-MIP is a pipeline for analyzing intron polymorphisms to identify species and study population genomics.

## Contribution

The pipeline introduces a scalable and reproducible method for analyzing MIPs across diverse taxa.

## Key findings

- The pipeline integrates tools like Cutadapt, FLASH, and SeekDeep for efficient intron region analysis.
- MIPs are effective for species identification, detecting cryptic species, and assessing population structure.
- The pipeline was demonstrated on teleost species and tested with representative datasets.

## Abstract

In this Research Note, we introduce Intronomics-MIP, a snakemake-based pipeline for the automated analysis of multi-locus intron polymorphisms (MIPs) using intron-targeted amplicon sequencing. Building on established methodologies, our pipeline integrates tools such as Cutadapt, FLASH, and SeekDeep to efficiently process and analyze highly variable intron regions. These MIPs serve as powerful multiple-allelic markers, primarily useful for distinguishing species, identifying cryptic species, disentangling species complexes and detecting hybridization, but can also be informative for assessing population structure without prior species knowledge. Our pipeline enhances reproducibility and scalability, making it adaptable to a wide range of taxa, with a specific demonstration on teleost species. We provide a comprehensive overview of the pipeline’s design, along with performance assessments using representative datasets.