7ff0c9ec-ce98-4e20-a316-b8b97fec0759 1.0 Metabarcoding Runner 2021-03-23 2019-07-04 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 available at: <a href="https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/67885733-f393-4a55-bdaa-999d0f3f83a0" target="_blank">https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/67885733-f393-4a55-bdaa-999d0f3f83a0</a>. Ana Filipa Filipe CIBIO-InBIO affilipe@cibio.up.pt Antonio José SÁENZ-ALBANÉS LifeWatch ERIC ICT Core aj.saenz@lifewatch.eu Lucia Vaira LifeWatch ERIC Service Centre lucia.vaira@lifewatch.eu ICT Core Group LifeWatch ERIC ICT Core ict.coordination@lifewatch.eu https://metadatacatalogue.lifewatch.eu/srv/api/records/7ff0c9ec-ce98-4e20-a316-b8b97fec0759/attachments/metagenomics.jpg metagenomics.jpg metagenomics remote sensing Bioinformatics NGS data Environmental DNA Metabarcoding pipeline Taxonomic assignment Metabarcoding IJI GPLv3 Fastq https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/f84e2694-c90c-4c70-a727-0bfc1f7c049f This is one of the three input files required for running this service. The fastq file contains DNA sequences generated from High Throughput Sequencing of eDNA samples. Input file Reference_db https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/64b81b5f-c788-45c6-935c-b99f3fcf9535 This is one of the three input files required for running this service. This file contains a list of species and reference genetic sequences that will be used for the taxonomic assignment of eDNA metabarcoding sequences. Input file Sample_metadata.tsv https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/c3739804-b8b6-42d0-8a25-06b361092703 This is one of the three input files required for running this service. 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. Input file Species_occ.csv https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/52be722a-4372-40fb-a91a-cf11332f80be 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. Output file Workflow Studio data processing data analysis data selection data access https://helpdesk.lifewatch.eu/ https://my.lifewatch.eu/workflow/create-workflow-from-template/metabarcoding-runner WWW:LINK-1.0-http--link Link to the service https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/67885733-f393-4a55-bdaa-999d0f3f83a0 WWW:LINK-1.0-http--link Link to the workflow