metagenomics mature cherry
Metagenome sequencing was performed on the DNBSEQ-T7 platform (Complete Genomics, San Jose, CA, USA) with a read length of 150 bp following the manufacturers instructions (custom by demand service). Data processing and functional annotation were performed following a pipeline workflow developed by the BGI manufacturer (Genomic Groups, China). In brief, after the sequencing is performed, preprocessing is necessary to obtain valid data (Clean Data) that can be used for subsequent analysis. This includes removing low-quality reads, reads with excessive N bases, and non-genomic sequences, primarily those introduced during library preparation (adapters, primers, and indexes). The quality control of sequencing reads, and removal of host reads was performed using the SOAPnuke (Chen et al., 2018). Further, Bowtie2 was used to align the sequences to the host genome, remove the aligned sequences (host), and generate clean Data (Langmead and Salzberg, 2012). This step involved the removal of 10% or more uncertain bases (N bases); the removal of reads containing sequencing adapter sequences (regions with 15 or more consecutive bases aligned to adapter sequences); and the removal of reads with over 50% low-quality bases (bases with a quality score below 20).