R course

Daniel Vaulot

2023-01-26

Metabarcode analysis - metaPR2

Outline

  • Intro to metaPR2

  • Visualization/Analysis

  • MetaPR2 in practice

Introduction to metaPR2

MetaPR2 - Datasets

OSD

MetaPR2 - Datasets

Tara Oceans

MetaPR2 - Datasets

Malaspina

MetaPR2 - Datasets

Others (41 total)

MetaPR2 - Taxonomy

Eight levels:

  • Kingdom: Eukaryota
  • Supergroup: Archaeplastida
  • Division: Chlorophyta
  • Class: Mamiellophyceae
  • Order: Mamielliales
  • Family: Bathycoccaceae
  • Genus: Bathycococcus
  • Species: B. prasinos

MetaPR2 - Visualization

Barplots

Maps - Dominant

Maps - Pie charts

Diversity

MetaPR2 - In practice

Help and Samples

Help

  • Read in detail

Sample table

  • dataset_name
  • paper (can be useful to read)
  • number of samples
  • number of ASVs
  • number of reads per sample (coverage)

Sample selection

  • Major datasets: OSD, Tara, Malaspina
  • By habitat: oceanic, coastal etc…
    • Start by “marine global V4”
    • Extend to other habitats/datasets
  • V4 vs V9
  • DNA vs. RNA
  • Ecosystems
  • Sustrate: water, ice, soil…
  • Size fractions: total, pico…
  • Depth level: surface, euphotic…
  • Minimum ASV: will filter out rare ASVs (e.g. 1000)
  • Selection can be saved (yaml file)

Taxonomy

  • Can select several taxa within one level
  • Press validate every time you need to refresh
  • Can exclude taxa to remove fungi, metazoa…
  • Can save taxonomy and reload taxonomy (yaml file)

Treemaps, Maps and Barplots

Treemaps

  • Left panel: abundance (number of reads)
    • Reads are “normalized” to 100
  • Right panel: diversity (number of ASVs)

Maps

  • Read information at top
    • Taxo level
    • Number of samples with/without taxa
  • Crosses where taxa absent
  • Map types
    • Dominant
    • Pie chart
  • Circle scale
    • Moving right increases size

Barplots

  • taxonomy vs. function
  • variables to use (but this depends on samples selected !)
    • fraction name
    • ecosystem
    • substrate
    • depth level
    • DNA_RNA
    • latitude
    • temperature
    • salinity
    • year, month, day for time series

Diversity

  • Hit “Compute…” after refreshing taxonomy
  • Time proportional to N samples and taxa
  • Information about
    • Number of samples
    • Number of taxa (ASVs)

Alpha diversity

  • X: Chao1, Shannon, Simpson (compare)
  • Discretize continuous Y
  • Change Y (see barplots)
  • Change shape
  • Change color

Beta diversity

  • Ordination method (difference ?)
  • Ordination distance (Bray, Jaccard…)
  • Change color and shape

Download

  • Download
    • datasets
    • samples
    • asv list with taxonomy
    • asv sequences

Only for those with extensive experience with data processing.

metaPR2