Glossary

Key Points

Metabarcoding Basics	Most metabarcoding pipelines include the same basic components Frequency tables are key to metabarcoding analyses
Demultiplexing and Trimming	First key point. Brief Answer to questions. (FIXME)
Denoising or clustering the sequences	Clustering sequences into OTUs can miss closely related species Denoising sequences can create overestimate diversity when reference databases are incomplete
Taxonomy Assignment	The main taxonomy assignment strategies are global alignments, local alignments, and machine learning approaches The main difference is that Naive Bayes requires the reference data to be trained, whereas Sintax looks for only kmer-based matches
Creating A Reference Database	First key point. Brief Answer to questions. (FIXME)
Statistics with R: Getting Started	Phyloseq has many functions to explore metabarcoding data Results from early lessons must be converted to a matrix Phyloseq is integrated with ggplot to expand graphic output
Statistics and Graphing with R	The Phyloseq package has many useful features to conduct statistical analyses of your data
Introduction to Qiime	Once you import your results into Qiime, you can run any analysis with that program The OTU fasta file that we created today are equivalent to ‘rep-seqs’ (representative sequences) in Qiime The frequency table we created is called a ‘FeatureTable’ in Qiime parlance

FIXME