- Authors:
-
Scapolatiello, A.; Boscari, E.; Schiavon, L.; Vitulo, N.; Congiu, L.
- Title:
-
Intronomics-MIP: a snakemake pipeline for analyzing multilocus intron polymorphisms in species identification and population genomics
- Year:
-
2025
- Type of item:
-
Articolo in Rivista
- Tipologia ANVUR:
- Articolo su rivista
- Language:
-
Inglese
- Referee:
-
No
- Name of journal:
- BMC RESEARCH NOTES
- ISSN of journal:
- 1756-0500
- N° Volume:
-
18
- Number or Folder:
-
1
- Page numbers:
-
1-8
- Keyword:
-
Bioinformatics pipeline; High-throughput DNA sequencing; Molecular markers; Multiple-SNP haplotypes; Non-model organisms; Teleost fishes
- Short description of contents:
- 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.
- Product ID:
-
145778
- Handle IRIS:
-
11562/1162114
- Last Modified:
-
May 15, 2025
- Bibliographic citation:
-
Scapolatiello, A.; Boscari, E.; Schiavon, L.; Vitulo, N.; Congiu, L.,
Intronomics-MIP: a snakemake pipeline for analyzing multilocus intron polymorphisms in species identification and population genomics
«BMC RESEARCH NOTES»
, vol.
18
, n.
1
,
2025
,
pp. 1-8
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