Evidence map›Paper›PMID 40325430›Full record

ArticleBMC research notes2025

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

A Scapolatiello, E Boscari, L Schiavon, N Vitulo, L Congiu

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Article in BMC research notes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

A ScapolatielloDepartment of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy. annalisa.scapolatiello@studenti.unipd.it.
E BoscariDepartment of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy.
L SchiavonDepartment of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy.
N VituloDepartment of Biotechnology, University of Verona, Strada le Grazie, 15, 37134, Verona, Italy.
L CongiuDepartment of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padua, Italy.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Genetics, PopulationGenomicsIntronsPolymorphism, GeneticAnimalsFishesSpecies SpecificityBioinformatics pipelineHigh-throughput DNA sequencingMolecular markersMultiple-SNP haplotypesNon-model organismsTeleost fishes

Identifiers

PMID40325430
PMCPMC12054228

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.