Bioscan biomonitoring workflow

This is the documentation for the metabarcoding workflows (bioscanflow) developed and used withing the framework of Biodiversity Genomics Europe (BGE). The documentation includes the following sections:

Sampling

1sampling.html

Sample prep.

2sample_prep.html

DNA extraction

3DNA_extraction.html

Library prep.

4amplicon_lib.html

Bioinformatics

6bioinfo.html

Examine metabarcoding outputs

7interpret.html

Contents

• What is a metabarcoding workflow?
  • Outputs
  • Reading the outputs
  • Sequence abundance ≠ biological abundance
  • Taxonomic assignments
  • Metabarcoding is not perfect
• BGE case studies | SOPs
  • High Mountain Systems - Arthropods
  • Pollinator Communities
  • Ecological Restoration - Soil Chronosequences
  • Detection of non-indigenous marine species from port water samples
• Sampling
  • Registering samples in PlutoF and PlutoF GO
  • Water
  • Soil
  • Malaise trap
• Sample prep. for DNA extraction
  • Water
  • Soil
  • Malaise trap
• DNA extraction
  • Water
  • Soil
  • Malaise trap sample
• Amplicon library preparation
  • 16S
  • ITS2
  • 18S
  • 12S
  • COI
• Bioinformatics
  • Arthropods/COI
  • Fungi/ITS
  • 16S/18S/12S
  • Identify and remove contaminants
  • Other taxonomy assignment tools
• Examine metabarcoding outputs
  • Examine outputs
  • Essential Biodiversity Variables of genetic composition
  • eDNA taxonomy validation (VAL_OTU_ID)
  • Hierarchical Modelling of Species Communities
• FAIR publication of eDNA results
  • Uploading sample records to ENA
  • Uploading raw sequence data to ENA
  • Uploading representative sequences of metabarcoding features to PlutoF
  • Publishing metabarcoding features in GBIF
• Additional resources

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