Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

Barzon, Luisa; Lavezzo, Enrico; Militello, Valentina; Toppo, Stefano; Palù, Giorgio

An aspect that should not be neglected when dealing with NGS data, is the bioinformatics analysis and issues concerning sequencing output. There are inherent strengths and weaknesses in the different platforms as reported in Table 1 . For example, 454 technology is well suited for small de novo sequencing projects and amplicon studies, given its read length output that presently reaches the average length of sequences produced with Sanger method. The main issue to be aware of concerns the homopolymer length, due to signal thresholding of the incorporated nucleotides. SOLiD platform is not presently suitable for amplicon studies due to the short read length, but exhibits an extremely high throughput capacity. Illumina has a superior read length and is not affected by homopolymers but, as SOLiD, shows low coverage of AT rich regions [134] . Other platforms present in Table 1 (with the exclusion of the GS Junior, which shares the same features of 454 FLX but has a lower throughput) are still in development and not yet evaluated in their diagnostic potential.