List of Training Materials¶
Background Material¶
Factors influencing course design¶
- Organisms
- Audience/Student expertise
- Course length
- Compute resources
- Trainer knowledge
- Environment/Biome
- Available Datasets
Links to resources that cover several for the above topics¶
Background¶
- Experimental Design
- Computer Literacy
- Cloud Computing
- Sequencing options
- Statistical power
Links to resources that cover several for the above topics¶
Pre-Processing¶
Data treatment/pre-processing¶
- Quality
- Filtering Reads
- Trimming Reads
- Contamination
- Barcodes / multiplexing
- Read Merging
Links to resources that cover several for the above topics¶
Assembly¶
- Short reads
- Long reads
- Hybrid
- Data reduction / Clustering / Dereplication
Links to resources that cover several for the above topics¶
Types of Analysis¶
Marker gene amplicons¶
- 16s rRNA, 18s rRNA, ITS1/2
- Taxonomic profiling
- OTU clustering
- taxonomy -> function inferences
Links to resources that cover several for the above topics¶
Shotgun metagenomics & metatranscriptomics¶
- To assemble or not?
- To gene call or not?
- Kmers (“reference-free”)
- Taxonomic profiling
- Coverage estimation
- Reference mapping / alignment
- Gene Catalogues
- Marker-Based approaches
- Read-based approaches
- Functional profiling/annotation
- Functional hierarchies / ontologies
- Depth comparisons
- Binning
- Whole genome assembly and evaluation
- Pathway Analysis / Metabolic modeling
- Cross assembly