ASV portal: an interface to DNA-based biodiversity data in the Living Atlas

• Published in: BMC Bioinformatics Vol. 24; no. 1; p. 6
• Main Authors: Prager, Maria, Lundin, Daniel, Ronquist, Fredrik, Andersson, Anders F.
• Format: Journal Article
• Language: English
• Published: London Springer Science and Business Media LLC 05.01.2023; BioMed Central; BioMed Central Ltd; BMC
• Subjects: Algorithms; Amplicon sequencing; Biodiversity; Biodiversity informatics; Bioinformatics; Biological diversity; Biological research; Biology (General); Biology, Experimental; Biomedical and Life Sciences; BLAST; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Computer applications to medicine. Medical informatics; Darwin core; Diversity of life; DNA; DNA - genetics; DNA Barcoding, Taxonomic; DNA sequencing; Ecology; eDNA; Ekologi; Life Sciences; Livets mångfald; Metabarcoding; Microarrays; Nucleotide sequencing; Online databases; QH301-705.5; R858-859.7; Software; Species occurrence; Web portals; Sweden; Metabarcoding; Darwin core; Amplicon sequencing; Biodiversity informatics; eDNA; BLAST; Species occurrence
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-022-05120-z

Background The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas. Results The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.