PAC-BIO seq of nosZ clade II in semi-arid cotton production
In Unix HPRC, cutadapt module loaded and demultiplexing conducted with no indels option. All remaining processing for these sequences conducted in R statistical package with the following packages: dada2, Biostrings, ShortRead, ggplot, reshape2, gridExtra, phyloseq. Removed primers (removeprimers function), checked sequence length with a histogram, filtered sequences with non-normal lengths (minimum 600, maximum 1000 for nosZ, filterandtrim function), dereplicated sequences (derap fastq function), learnerrors function with option, errorEstimationFunction = PacBioErrfun, to learn error designations, then dada function was used to denoise the data.