Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality DOI Creative Commons
Xin‐Yi Chua,

Louise Ord,

Stephen J. Bent

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(6)

Published: Nov. 1, 2024

ABSTRACT The success of amplicon sequencing studies environmental DNA (eDNA) depends on the choice primer pairs used to select taxa‐specific regions for amplification then characterize sample composition. This paper presents practical methods visualize extent which different can differentiate taxonomic groups, enabling researchers assess primers might be best suited a study or environment interest. These also review annotations in genomic reference sequence databases. We apply concept barcoding gaps metabarcoding multiple species leverage data sequences previously characterized specimens. Since sets are large and complex, we provide simple intuitive method navigate subsets containing conflicting ambiguous relationships between information classification. demonstrate how use gap visualization segmentation comparing well discriminate interest, detecting anomalies annotation. show these enable survey design make fundamental molecular resources more accessible wider research audience beyond bioinformaticians scientists.

Language: Английский

Barcoding of Italian mosquitoes (BITMO): generation and validation of DNA barcoding reference libraries for native and alien species of Culicidae DOI Creative Commons
Beatrice Bisaglia, Michele Castelli, Laura Soresinetti

et al.

Parasites & Vectors, Journal Year: 2024, Volume and Issue: 17(1)

Published: Sept. 28, 2024

Language: Английский

Citations

0
Using Gap Visualization to Navigate Multivariate Metabarcode Data, Select Primer Pairs, and Enhance Reference Data Quality DOI Creative Commons
Xin‐Yi Chua,

Louise Ord,

Stephen J. Bent

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(6)

Published: Nov. 1, 2024

ABSTRACT The success of amplicon sequencing studies environmental DNA (eDNA) depends on the choice primer pairs used to select taxa‐specific regions for amplification then characterize sample composition. This paper presents practical methods visualize extent which different can differentiate taxonomic groups, enabling researchers assess primers might be best suited a study or environment interest. These also review annotations in genomic reference sequence databases. We apply concept barcoding gaps metabarcoding multiple species leverage data sequences previously characterized specimens. Since sets are large and complex, we provide simple intuitive method navigate subsets containing conflicting ambiguous relationships between information classification. demonstrate how use gap visualization segmentation comparing well discriminate interest, detecting anomalies annotation. show these enable survey design make fundamental molecular resources more accessible wider research audience beyond bioinformaticians scientists.

Language: Английский

Citations

0