Table 2.

Advantages and disadvantages of sequencing technology in the detection of different pathogens.

Pathogen	Advantage	Disadvantage	Sequencing approach	References
Bacteria	Simplified bioinformatics Amplifies the amount of microorganisms present and targets Reduced price	Only Bacteria identification Particular microbes Can still miss some species due to primer mismatches Scarce copy of pathogen sequences may be harder to detect.	tNGS (16S rRNA)	Petersen et al. (2019)
Fungi	Reduced price Better sensitivity and massive information More speed Simplified bioinformatics The ability of amplified most of the fungus is available.	Still miss some species due to primer mismatches Particular to a subgroup of parasites and fungus Scarce copy of pathogen sequences may be harder to detect	tNGS (18S rRNA gene/ITS gene sequence)	Xing et al. (2022), Arastehfar et al. (2019)
Virus	Higher sensitivity and amount of data allows de novo assembly and even reads level detect Potential to detect the full spectrum of viruses, including unknown and unexpected viruses Allowing for the thorough identification of minority variants, which represents a clear advantage over direct (Sanger) sequencing Detection of pathogens that do not rely on references or amplification	Assembly and characterization of complex/highly repetitive genomic regions Reconstruction of complete “real” viral haplotypes	WGS; mNGS	Barzon et al. (2011), Quer et al. (2022) Houldcroft et al. (2017)