Getting ready

For this recipe, we need the Bioconductor dada2 package and the CRAN cowplot package. We'll use some metagenomic sequence reads from the Short Read Archive experiment SRR9040914, in which the water from a tidal marine lake at a tourist center was examined for species composition because people were tossing coins into it and making wishes. We will use twenty fastq files of 2,500 files each, each compressed and available in this book's repository at datasets/ch5/fq. This is a small subset of the full set of Illumina reads. We'll also need the datasets/ch5/rdp_train_set_14.fa file, which is one of the sets of 16S sequences maintained as training sets by the dada team. See more training sets at http://benjjneb.github.io/dada2/training.html

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