Glossary

Key Points

Demultiplexing Reads	Barcodes let us sequence many samples at the same time and separate them computationally Most pipelines require demultiplexing reads as a first step
Sequnece quality control	FIXME: ADD KEY POINT FIXME: ADD KEY POINT
Counting microbes with QIIME2-Deblur	FIXME: ADD KEY POINT FIXME: ADD KEY POINT
Counting microbes with DADA2	FIXME: ADD KEY POINT FIXME: ADD KEY POINT
Counting microbes with mothur	FIXME: ADD KEY POINT FIXME: ADD KEY POINT

Beta diversity	Beta diversity measures the diversity between samples in a dataset The most common beta diversity measures are Bray-Curtis, Weighted/Unweighted Unifrac, and NMDS Beta diversity is usually displayed as a principal coordinates plot Cluster analysis can identify groups of samples, but care must be taken to be sure the groups are meaningful
Finding Differentially Abundant Microbes	FIXME: ADD KEY POINT FIXME: ADD KEY POINT

Amplicon: A piece of DNA made by amplifying (making many copies) of a specific target site.
Illumina: A common method of DNA sequencing that generates millions of short (<500 base-pair) sequences.
Metagenomics: Analysis of random segments of DNA from a microbial community instead of specific amplicons.
mothur: A software suite commonly used for amplicon analysis.
PCR: Polymerase Chain Reaction, the most common way to amplify small amounts of DNA and prepare them for sequencing.
Primers: The short pieces of synthetic DNA used to specify the target for amplification.
QIIME 2: A software suite commonly used for amplicon analysis.