User:R. Eric Collins/GenomicsTutorial/Metagenomics

8 February 2011 Metagenomics Tutorial -- McGill University

Metagenome Sequencing/Assembly

SOLiD/Illumina

Illumina video SOLiD video

Usage Scenario: de novo sequencing of ~5Mb bacterial isolates at 20--30x coverage

A SOLiD 3Plus slide would give enough data for >48 samples combined. Costs with library preparation are $1,800 per sample. For sequencing on a full slide, total costs are $12,500.00 regardless of the number of barcoded samples you have in the pool.

On the Illumina GAII you could have up to 6 samples in the same pool. Costs for each set of 6 samples, including library prep and sequencing, are $14,200.00 for 2x100bp reads

Usage Scenario: transcriptional profile sequencing on environmental samples

Library preparation and sequencing are $3,600.00 for Illumina 100-bp. Costs with library preparation are $1,800 per sample. For sequencing on a full slide, total costs are $12,500.00 regardless of the number of barcoded samples you have in the pool.

Next Next Generation Sequencing

• Video: Ion Torrent
• Video: Helicos
• Video: Pacific Biosciences

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Ecology

Phylogenetic Diversity

• general: MOTHUR
• hypervariable tags: VAMPS -- The Visualization and Analysis of Microbial Population Structures

Metabolic Diversity & Functional Genomics

• KEGG pathways
• megablast
• alignments

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Mobile Genetic Elements

Phage/Viruses

• Phage Finder
• PHACCS -- PHAge Communities from Contig Spectrum

Plasmids

• Plasmid Genome Database
• List of plasmids at NCBI

Horizontal Gene Transfer

• genomic islands: Islandpath
• database: HGT-DB
• detection: DarkHorse HGT Candidate Resource

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