2.1.6. Bioinformatics for Ion Torrent

After generation, sequencing reads were filtered for quality and binned according to the Ion Xpress barcode using Ion Torrent Suite software version 5.10.0. Sequencing reads in FASTQ format were further processed using web-based Galaxy software [13]. First, raw FASTQ files were normalized using the FASTQ groomer tool function. Next, each barcoded read was trimmed to remove the primer sequence and subsequently filtered to the expected size of the 16S gene target. After this level of processing, the sequence reads were concurrently compared to the SILVA 16S database using bowtie 2 software [14,15]. This yielded a call to species or genera level and the number of times each sequence matched the database (hit-rate). When multiple calls to a genus were made, the number of hits was added accordingly. These numbers were then converted to percentage of total to give an overall ratio of the sequenced sample.