User:R. Eric Collins/GenomicsTutorial/Genomics
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7 February 2011 -- Genomics Tutorial -- McGill University
Genome Sequencing
Instrument: Roche 454
Each full 454 plate generates about 300-500 Mbases of raw sequence data
Usage Scenario: hypervariable tag sequencing (e.g. V6 of bacterial 16S rRNA) on environmental samples
- add Titanium fusion primers to your PCR primers
- barcode many (>48) samples for sequencing as a pool in the same plate
- send off the pool of samples
- total cost is $7,800.00
Usage Scenario: de novo genome sequencing of 6 bacterial isolates (5Mb) at 10--12x coverage
- the most cost effective way to perform this experiment is to barcode these samples and sequence them as a pool.
- total costs per set of 6 samples is $12,000.00, including library preparation and sequencing.
de novo Assembly
- Assembly Primers: CBDB NCBI
- Annotation Pipelines: MicroScope MiGAP DIY Genomics IMG/mer JCVI Service BASys GenDB SABIA
Assembly with Reference Genome
- whole genome alignment: MUMmer
View reads against reference
Sequence Clustering
Algorithms
- BLAST
- blast-clust
- MCL and TribeMCL
Orthologous Groups
Metabolic Pathways/Predictions
Phylogenetics
Find a gene of interest
- KEGG or IMG or NCBI
- Find the paper at NCBI: An ice-binding protein from an Antarctic sea ice bacterium
- All Links From This Record --> Protein
- Analyze this sequence --> Run BLAST
- Run against 'nr' database using default parameters
- click [Distance tree of results]
Get an alignment
- IMG or NCBI or EBI
Infer a Phylogeny
- IMG or EBI
View a Phylogenetic Tree
- Jalview or iTol
