Genotype by Sequencing: Glossary

Raw data should always be checked with FastQC.

Assigning reads to specific samples is called demultiplexing

process_radtags is the built in demultiplexing tools of Stacks and it includes some basic quality control

-M is the main parameter to optimise when identifying variants de-novo using Stacks

Optimisation can often be performed with a subset of the data

SLURM scripts are the way to harvest the cluster’s potential by running jobs

Reference genomes, even of poor quality or from a related species are great for SNP identification

Reference-based SNP calling takes the guess work of distance between and within loci away by mapping reads to individual location within the genome

SNP filtering is about balancing signal vs noise

Populations is the stacks implemented software to deal with filtering of SNPs

Principal component analysis (PCA) and Structure are easy visualisation tools for your samples