Metagenomics Image: Iverson et al. 2012, Science.

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Presentation transcript:

Metagenomics Image: Iverson et al. 2012, Science

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

Metagenomics Assembly Binning Annotation/Analysis

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

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

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

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

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