2.7. Sequencing Data Quality Control

Quality control of the raw FASTQ files was performed using KneadData v. 0.6.1. Human reads were removed with Trimmomatic v. 0.36; the reads were quality trimmed by removing the Nextera adapter sequences, leading and trailing bases with a Phred score below 20, and trailing bases in which the Phred score over a window of size 4 drops below 20. Trimmed reads shorter than 100 bases were discarded. Reads that mapped to the human reference genome GRCh38 (Bowtie2 v. 0.2.3.2 using default settings) were discarded. Only read pairs in which both reads passed filtering were retained; these were classified as high-quality non-host (HQNH) reads.