User:R. Eric Collins/GenomicsTutorial/Metagenomics

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

Phylogenetic Diversity

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

Metabolic Diversity & Functional Genomics

 * KEGG pathways
 * megablast
 * alignments

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