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: ```sh 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)**: - [x] metabarcoding: decontamination and filtering, - [x] metabarcoding: alpha diversity, - [x] metabarcoding: alpha diversity vs locality, - [x] metabarcoding: beta diversity vs locality, - [x] metabarcoding: beta diversity vs locality (make a new plot with barycenters), - [x] metabarcoding: use 20 taxonomic fields and weighted assignments, - [ ] metabarcoding: taxonomy and functions (nitrogen cycle), - [x] 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,