frederic-mahe / Oracle-Burkina-Faso-Soil-Metagenomics

Project Oracle: metagenomics of agricultural soils from Burkina Faso

Project Oracle

Metagenomics of agricultural soils from Burkina Faso

Sampling and sample processing

• Sample collection (2017),
• geographical coordinates,
• DNA extraction,
• Shotgun sequencing (Illumina NovaSeq),
• 16S and ITS2 amplification and sequencing (Illumina MiSeq)

(to be written)

From raw sequences to annotated occurrence tables

(scripts are available, will be added later)

Statistical analysis

(see the Rmarkdown scripts, starting with src/04_numerical_ecology.Rmd)

Note that library functions are noted as package::function() (for example, vegan::diversity()), except for tidyverse functions and base packages.

Taxonomy

temporary code to extract and prepare the Silva taxonomy:

cd ./data/Silva/

zgrep "^>" SILVA_138.1_SSURef_NR99_tax_silva.fasta.gz | \
    sed 's/^>// ; s/ /\t/1' > SILVA_138.1_SSURef_NR99_tax_silva.txt

Roadmap (16S):

• metabarcoding: decontamination and filtering,
• metabarcoding: alpha diversity,
• metabarcoding: alpha diversity vs locality,
• metabarcoding: beta diversity vs locality,
• metabarcoding: beta diversity vs locality (make a new plot with barycenters),
• metabarcoding: use 20 taxonomic fields and weighted assignments,
• metabarcoding: taxonomy and functions (nitrogen cycle),
• metagenomics shotgun: filtering,
• metagenomics shotgun: turn NMDS plot into a function,
• metagenomics shotgun: use the metabarcoding taxonomic framework,
• metagenomics shotgun: alpha diversity,
• metagenomics shotgun: alpha diversity vs locality,
• metagenomics shotgun: beta diversity vs locality,