1. Metagenomics
Image: Iverson et al. 2012, Science

2. Metagenomics Definition
Direct sequencing and analysis of environmental samples that contain DNA from numerous organisms.

3. Metagenomics
Assembly
Binning
Annotation/Analysis

4. Metagenomics Assembly
Challenges and contrasts with conventional genome assembly
Extreme variation in levels of coverage
Populations of similar but non-identical sequences
Metagenome assemblers
metaSPAdes
IDBA-UD
Ray Meta
MetaVelvet

5. Metagenomics
Binning
Grouping assembled contigs into “bins” that correspond to a single species or taxon
Criteria
Assembly-Based: Read depth and paired-end connections
Composition-Based: GC content and other measures of nucleotide composition
Homology-based: Sequence similarity to known taxa

6. Metagenomics Binning Software abundanceBin iClaMS MaxBin MBBC MEGAN
MetaBat
MetaCluster
Phylothia
PhymmBL
S-GSOM
SPHINX
TETRA
CONCOCT
SOrt-ITEMS

7. Metagenomics Annotation and Analysis
Who’s there? (taxonomic identification)
What are they doing? (functional gene annotaiton)

8. Exercise ~/TodosSantos/metagenomic_binning
Summarize GC content and coverage for each contig from a ”simple” metagenome assembly – DNA isolated from whole whiteflies including associated bacteria.
Use BLAST to compare contigs to representative bacterial taxa.
Visualize metagenomic binning by plotting data in R.
Image: Gottlieb et al. 2010