2.4 Data processing and analysis
High-quality sequencing data were generated after removing low quality,
low complexity, and shorter reads. The data mapped to the human
reference genome (hg19) were excluded using a powerful alignment tool
called Burrows-Wheeler Alignment to elimiĀnate the effect of the human
sequences. The database used for the present study includes 6039
bacteria, 4945 viruses, 1064 fungi, which all related to human disease.
Finally, the mapped data were processed after filtering out duplicate
reads for advanced analysis. The SoapCoverage from the SOAP website was
used to calculate the sequence depth and genomic coverage for each
species.