Metadata Catalogue
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
- Date ( Publication)
- 2021-03-23
- Date ( Creation)
- 2019-07-04
- Status
- Under development / Pre operational
- Keywords
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metagenomics
- Keywords
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remote sensing
- Keywords
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Bioinformatics
- Keywords
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NGS data
- Keywords
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Environmental DNA
- Keywords
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Metabarcoding pipeline
- Keywords
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Taxonomic assignment
- Keywords
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Metabarcoding
- Keywords
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IJI
- Access constraints
- License
- Use limitation
-
The final license will be available soon.
- Operation name
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Fastq
- Description
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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
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Input file
- Operation name
-
Reference_db
- Web site
- Description
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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
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Input file
- Operation name
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Sample_metadata.tsv
- Description
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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
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Input file
- Operation name
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Species_occ.csv
- Description
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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
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Output file
- Service Category
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data processing
- Service Category
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data analysis
- Service Category
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data selection
- Service Category
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data access
- Service Language
- eng
- Service TRL
- TRL 7 – System prototype demonstration in operational environment
- Service Helpdesk
Metadata
- File identifier
- 7ff0c9ec-ce98-4e20-a316-b8b97fec0759 XML
- Metadata language
- en
- Hierarchy level
- Service
- Metadata Schema Version
-
1.0
