User:R. Eric Collins/GenomicsTutorial/Metagenomics

From OpenWetWare
Jump to: navigation, search

8 February 2011 Metagenomics Tutorial -- McGill University

Metagenome Sequencing/Assembly

SOLiD/Illumina

Illumina video SOLiD video

barcoding/multiplexing
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
quality control
resequencing/scaffolding
mutation

Ecology

Phylogenetic Diversity
Metabolic Diversity & Functional Genomics
  • KEGG pathways
  • megablast
  • alignments

Mobile Genetic Elements

Phage/Viruses
Plasmids
Horizontal Gene Transfer