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Environmental DNA (eDNA) Workflows & Biodiversity Calls Training | DADA2/VSEARCH, BLAST/IDTAXA, Occupancy & MIxS

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Microbiome, Metagenomics & Environmental Bioinformatics >> Environmental DNA (eDNA) Workflows & Biodiversity Calls Training | DADA2/VSEARCH, BLAST/IDTAXA, Occupancy & MIxS

Environmental DNA (eDNA) Workflows & Biodiversity Calls — Hands-on

Build end-to-end environmental DNA (eDNA) pipelines from field sampling to defensible biodiversity calls. Learn contamination-safe collection and extraction, marker/primer selection, sequencing and QC, ASV/OTU inference, taxonomic assignment against curated references, and decision-grade reporting with occupancy/detection models and uncertainty quantification.

Environmental DNA (eDNA) Workflows & Biodiversity Calls
Help Desk · WhatsApp
Session 1
Fee: Rs 8800
Field Sampling, Controls & Wet-Lab
  • Sampling design & logistics
    • water/soil/air/sediment filtration (Sterivex/filters) preservation & transport
  • Contamination control & inhibitors
    • field/kit blanks, negatives dedicated clean areas PCR inhibitor mitigation
  • Markers & primers
    • 12S/16S/18S/COI amplicon vs capture qPCR/ddPCR assays
Session 2
Fee: Rs 11800
QC, Denoising & Taxonomic Assignment
  • Read processing & ASV/OTU calling
    • cutadapt/fastp, merging DADA2/UNOISE/VSEARCH chimera & LULU curation
  • Reference DBs & assignment
    • BOLD/MIDORI/PR2/SILVA BLAST LCA / IDTAXA naive Bayes (q2-classifier)
  • Decontamination & tag-jump checks
    • decontam prevalence/freq min read thresholds replicate concordance
Session 3
Fee: Rs 14800
Biodiversity Metrics & Occupancy Models
  • Diversity & community analyses
    • alpha/beta; Hill numbers rarefaction & coverage indicator species tests
  • Detection/occupancy modeling
    • unmarked/occu (R) false pos/neg handling replicate design power
  • qPCR/ddPCR quant & thresholds
    • std curves & LoD/LoQ copy→abundance heuristics decision thresholds
Session 4
Fee: Rs 18800
Mapping, Standards & Reproducible Reporting
  • Geospatial outputs & dashboards
    • QGIS/leaflet maps heatmaps & range overlays report-ready figures
  • Standards & data submission
    • MIxS & metadata ENA/SRA; GBIF/OBIS refs audit trails & SOPs
  • Ethics, permits & sensitive taxa
    • endangered species privacy biosecurity considerations stakeholder-ready summaries


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