Amplicon analyses¶
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¶
Learning objectives¶
- Define a marker gene and its taxonomic relevance.
- Distinguish between amplicon vs. shotgun approach.
- Apply a marker gene analysis workflow
- Analyse the taxonomic composition of an environment.
- Interpret results in biological context
- Describe and execute an amplicon workflow
- Install software for amplicon analysis
- Assemble paired-end reads
- Execute a shell script to automate a process
- Describe input and output files for amplicon workflows and scripts
- Describe the structure and components of a good mapping/metadata file
- Move sequences from compute resources to local computer
- Obtain summary information about sequence files (fasta, fna, fastq)
- Define operational taxaonomic units (OTUs)
- Align sequences, assign taxonomy, and build a tree with representative sequences from OTU definitions
- Calculate similarity of two samples (similarity matrices)
- Visualize comparative diversity across a priori categorical groups
- Convert .biom formatted OTU tables to text files for use outside of QIIME