Fred's metabarcoding pipeline: from raw fastq files to an occurrence table at light-speed
This is a work in progress. A less up-to-date pipeline is described here.
The goal is to identify sequence variants, possibly down to a single-nucleotide difference when necessary, and to produce a clean, ready-to-use occurrence table (number of observations of each sequence variant in each sample).
((BASH_VERSINFO[0] <= 4)) && echo "error: the shell you are using is too old"