Exploring microbial communities in the human gut, on plant roots, or in soil and water samples.
→ Metagenomics and the microbiome
Sequence data analysis
→ BLAST → Bowtie2 → SAMtools → Assembly → Shotgun sequencing → 16S tools → Ubuntu / Linux server
→ Strain-level resolution → 16S OTUs
→ Phylogenetic trees → Horizontal gene transfer
Resistance & Resilience
Coverage, quality measures, normalization