• LifeWatch ERIC Metadata Catalogue
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Metabarcoding Runner

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.

Default

Identification

Date ( Publication )
2021-03-23
Date ( Creation )
2019-07-04
Status
Under development / Pre operational
Version
1.0
Keywords
Bioinformatics
Keywords
NGS data
Keywords
Environmental DNA
Keywords
Metabarcoding pipeline
Keywords
Taxonomic assignment
Keywords
Metabarcoding
Keywords
IJI
Access constraints
License
Use limitation
The final license will be available soon.
Principal investigator
  CIBIO-InBIO - Ana Filipa Filipe
Custodian
  LifeWatch ERIC ICT Core - Antonio José SÁENZ-ALBANÉS
Publisher
  LifeWatch ERIC Service Centre - Lucia Vaira
Principal investigator
  LifeWatch ERIC ICT Core - Juan Miguel GONZÁLEZ-ARANDA
 
Protocol
DOI
Operation name
Fastq
Web site
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/f84e2694-c90c-4c70-a727-0bfc1f7c049f
Description
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.
Function
Input file
Operation name
Reference_db
Web site
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/64b81b5f-c788-45c6-935c-b99f3fcf9535
Description
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.
Function
Input file
Operation name
Sample_metadata.tsv
Web site
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/c3739804-b8b6-42d0-8a25-06b361092703
Description
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.
Function
Input file
Operation name
Species_occ.csv
Web site
https://metadatacatalogue.lifewatch.eu/srv/eng/catalog.search#/metadata/52be722a-4372-40fb-a91a-cf11332f80be
Description
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.
Function
Output file
Service Category
data processing
Service Category
data analysis
Service Category
data selection
Service Language
eng
Service TRL
TRL 7 – System prototype demonstration in operational environment
 

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