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  • This is one of the three input files required for running Step 1 (Metabarcoding Runner) of the Metabarcoding workflow. This file contains a list of species and reference genetic sequences that will be used for the taxonomic assignment of eDNA metabarcoding sequences. The other two input files for Step 1 are the "Fastq" file with sequences generated from High Throughput Sequencing of eDNA samples and the "Sample_metadata" with eDNA samples information.

  • This is the output file of Step 1 (Metabarcoding Runner) and the input file of Step 2 (Metabarcoding Syntax Normalizer) for the Metabarcoding workflow. This file is a taxa table containing the number of DNA sequences assigned to each taxon detected using High Throughput Sequencing of environmental DNA samples.

  • This is one of the three input files required for running Step 1 (Metabarcoding Runner) of the Metabarcoding workflow. The fastq file contains DNA sequences generated from High Throughput Sequencing of eDNA samples. The other two input files for Step 1 are the "Reference_db" and the "Sample_metadata" containing respectively the reference genetic sequences for the taxonomic assignment and the eDNA samples information.

  • This is one of the three input files required for running Step 1 (Metabarcoding Runner) of the Metabarcoding workflow. This file in Darwin Core format (https://dwc.tdwg.org/terms/) contains eDNA sample collection information including the location and the geographical coordinates of the eDNA sampling sites. The other two input files for Step 1 are the "Fastq" file with sequences generated from High Throughput Sequencing of eDNA samples and the "Reference_db" with reference sequences for the taxonomic assignment of eDNA sequences.

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    This dataset is based on the Atlas of Amphibians and Reptiles of Portugal published by ICNF in 2008. The publication of this document is related to the implementation of the National Strategy for the Conservation of Nature and Biodiversity, whose 5th strategic option concerns development throughout the national territory of specific actions for the conservation of species and habitats, defining as one of the action directives the elaboration of several distribution atlases. The Atlas shows, according to the record of observations made up to the date of its publication, the distribution, in Portugal, of amphibians and reptiles that are autochthonous in the Portuguese territory, and also exotic species existing in the wild: 17 species of amphibians; 30 species of terrestrial reptiles; and 5 species of sea turtles. The original publication presents, for each of the species, a sheet with the characterization of the species and notes on the main threats and measures for its conservation.

  • This service aims to compute a list of taxa IDs detected from metabarcoding sequences of environmental DNA (eDNA) samples. This service contains eight substeps (1.1 to 1.8) implemented as a unique step. The eight substeps perform (1) sequencing error correction (using BayesHammer-SPAdes); (2) pairwise alignment, (3) pre-filtering, (4) dereplication, (5) attribute filtering, (6) clustering and OTU tab-producer (using OBITools); (7) taxonomic assignment (using blastn); (8) OTUs table generator. Several types of eDNA samples can be processed (i.e. water, feces, soil). It represents the Step 1 of the Metabarcoding Workflow within the Internal Joint Initiative.

  • This service intersects the map(s) (geographical spatial polygons) from GBIF occurrence(s) with the locations of a list of taxa detected from eDNA metabarcoding and which were not included in the NIS checklist to verify if such eDNA detection(s) is/are likely to be new NIS detected in that location from eDNA sequences. It represents the Step 5 of the Metabarcoding Workflow within the Internal Joint Initiative.

  • This service aims at checking which taxa detected and identified from eDNA metabarcoding sequences are listed as NIS and which taxa are not (i.e. native or unrecorded NIS). This service uses available GBIF (Global Biodiversity Information Facility) records of NIS for each Country provided by the Invasive Species Specialist Group (ISSG). it checks if a species is present in the checklist and if this is the case, the species is flagged as being invasive for that country by adding 1 (yes) or 0 (no) to the column isInChecklist of the data frame, and the checklist key or a note to the ref_checklistKey column, for the corresponding cases. It represents the Step 3 of the Metabarcoding Workflow within the Internal Joint Initiative.

  • This service extracts from GBIF (Global Biodiversity Information Facility) taxa occurrence records that were not classified as NIS in Step 3 (GBIF NIS Verifier) of the Metabarcoding workflow. This step aims to verify if eDNA detections were identified outside the known distribution range using GBIF occurrences records. Additionally, for such eDNA detections, this step produces a geographical spatial polygon based on occurrence records available in GBIF. It represents the Step 4 of the Metabarcoding Workflow within the Internal Joint Initiative.

  • This service represents the Step 2 of the Metabarcoding Workflow within the Internal Joint Initiative. It aims at converting the CSV into rdata. It takes as input the Species_occ.csv file (output of the Step 1 Metabarcoding Runner), verifies the checklists available for each country and retrieves the first one. It produces two rdata files, that will be the inputs for the Step 3 GBIF NIS Verifier of the Metabarcoding workflow.