About the Swedish ASV portal

The portal of Swedish Amplicon Sequence Variants (ASVs) is an interface to sequence-based observations in the Swedish Biodiversity Data Infrastructure (SBDI). In addition to a database of amplicon sequence variants (ASVs) and a web interface, we provide a step-by-step guide(Link opens in a new tab) to submitting raw sequence data to ENA, and a pipeline(Link opens in a new tab) (developed in the nf-core collaboration) for denoising and taxonomic annotation of metabarcoding data.

Flow of metabarcoding data in SBDI: A sequencing service provider, such as NGI, delivers sequencing data to the user. The user submits raw sequencing data and contextual data to ENA (see our guide(Link opens in a new tab)), denoises the data using e.g. nf-core/ampliseq (Link opens in a new tab) , and submits the denoised data (ASVs and their counts in different samples, and contextual data) to the ASV portal. Metabarcoding data in the ASV database/Bioatlas can be searched and downloaded using the portal or using the SBDI4R package in R.

Why publish data in SBDI?

By publishing your data in the Swedish ASV database and Bioatlas your data will be easily reusable by others and can be seamlessly analysed in conjunction with other datasets in the Bioatlas. The ASVs will be regularly re-annoted as new reference database versions are released; thus your data will be updated with the latest taxonomic information. The ASV database also provides a complement to sequence repositories such as ENA or NCBI that typically only store raw sequencing data. Data in the Bioatlas is further regularly integrated in GBIF and therefor your metabarcoding-based biodiversity data will contribute to global knowledge about biodiversity.

Available data

Currently, we support inclusion of ASVs from the 16S rRNA gene for prokaryotes, the 18S gene for eukaryotes, the internal transcribed spacer (ITS) for fungi, and the COI cytochrome c oxidase I (COI) for metazoans. Other markers can be included on request. Read more about ASV taxonomy in SBDI here.

Marker genes and taxa currently represented in the ASV database

Marker Domains/Kingdoms/Supergroups* # Datasets # Phyla # Classes # Orders # Families # Genera # Species # ASV:s
16S rRNA Archaea, Bacteria, Unassigned 2 96 209 613 1343 3334 5818 41355
18S rRNA Amoebozoa, Archaeplastida, CRuMs, Cryptista, Cryptista:nucl, Eukaryota_X, Excavata, Haptista, Obazoa, Provora, TSAR, Unassigned 3 27 169 356 725 1479 2091 13976
COI Animalia, Chromista, Plantae, Unassigned 2 16 31 49 77 88 95 382
ITS|LSU rRNA Fungi 3 13 43 98 202 297 434 1640

* To accommodate data from different reference databases, and to facilitate data transfer to the Bioatlas and GBIF platforms, we group GTDB domains and PR2 supergroups together with UNITE and BOLD BIN kingdoms here. Read more about ASV taxonomy in SBDI.

We are currently working on improving the accessibility of this website. Please contact SBDI support with any questions or suggestions!