- Autori:
-
Scapolatiello, A.; Boscari, E.; Schiavon, L.; Vitulo, N.; Congiu, L.
- Titolo:
-
Intronomics-MIP: a snakemake pipeline for analyzing multilocus intron polymorphisms in species identification and population genomics
- Anno:
-
2025
- Tipologia prodotto:
-
Articolo in Rivista
- Tipologia ANVUR:
- Articolo su rivista
- Lingua:
-
Inglese
- Referee:
-
No
- Nome rivista:
- BMC RESEARCH NOTES
- ISSN Rivista:
- 1756-0500
- N° Volume:
-
18
- Numero o Fascicolo:
-
1
- Intervallo pagine:
-
1-8
- Parole chiave:
-
Bioinformatics pipeline; High-throughput DNA sequencing; Molecular markers; Multiple-SNP haplotypes; Non-model organisms; Teleost fishes
- Breve descrizione dei contenuti:
- 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.
- Id prodotto:
-
145778
- Handle IRIS:
-
11562/1162114
- ultima modifica:
-
15 maggio 2025
- Citazione bibliografica:
-
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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