Sequence data preprocessing and bioinformatics approaches
Fastp (version 0.14.1) was used to assess the quality of the raw
sequences using a sliding window (-W4-M20). Primers were removed using
cutadapt software (Martin 2011). The Usearch fastq_mergepairs command
was used to merge paired-end clean reads with a minimum of 16 bp
overlap, the maximum mismatch allowed in the overlap region was 5 bp,
and the spliced sequences were called raw tags. Fastp (version 0.14.1)
was then used to assess the quality of the raw tags using a sliding
window (-W4-M20) to obtain the paired-end clean reads. Sequences with
more than 97% similarity were classified as the same OTU.