- Organisms
- Audience/Student expertise
- Course length
- Compute resources
- Trainer knowledge
- Environment/Biome
- Available Datasets
- Experimental Design
- Computer Literacy
- Cloud Computing
- Sequencing options
- Statistical power
- Morgan Langille
- TGAC
- VanHijum tutorial
- Linux from BAS
- Linux from TGAC
- UC Davis Korf Lab
- EDAMAME Shell
- Software Carpentry Shell
- Python
- Github
- Data Carpentry Automation
- EDAMAME Cloud Computing
- Quality
- Filtering Reads
- Trimming Reads
- Contamination
- Barcodes / multiplexing
- Read Merging
- Short reads
- Long reads
- Hybrid
- Data reduction / Clustering / Dereplication
- 16s rRNA, 18s rRNA, ITS1/2
- Taxonomic profiling
- OTU clustering
- taxonomy -> function inferences
- 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
- John Parkinson
- Reference Tutorial
- BioMAS
- Morgan Langille metagenomic tutorial
- Metagenomics Crash Course
- CABBIO
- TGAC
- Metadata integration
- Sample comparison
- Ecological measurements/indexes
- Multivariate and comparative statistics
- Machine Learning