Splitting sequence files into OTUs can be done using the following steps:

1. Load the data and compute the OTUs:

library(kmer)
library(magrittr)
library(ape)
seqs <- ape::read.fastq(file.path(getwd(), "datasets", "ch5","fq", "SRR9040914ab.fq.gz")
otu_vec <- otu(seqs, k = 6, threshold = 0.99 )

2. Count the frequency of each OTU cluster:

data.frame(
    seqid = names(otu_vec), 
    cluster = otu_vec, 
    row.names = NULL) %>% 
dplyr::group_by(cluster) %>% 
dplyr::summarize(count = dplyr::n() )