Table 1.
Comparison between Next Generation Sequencing technique and Microarray technique.
| Next generation sequencing | Microarray |
|---|---|
| Advantages | |
| Species- or transcript-specific probes are not required in the case of NGS technology. | Specific probes are required in the case of microarray technologies. |
| NGS technology computes the sequencing read counts, analyzing the result for studying gene expression. | Gene expression measurement based on array hybridization technology is restricted by background and signal saturation noise. |
| NGS shows increased specificity and sensitivity for wide range of applications. | Specificity and sensitivity is low as compared to NGS for identifying differentially expressed genes. |
| Sequencing coverage depth is high in NGS technology facilitating the detection of rare or single transcripts per cell as well as in identifying weakly expressed genes. | Rare and low-abundance transcripts cannot be easily detected and are lost using microarray technology. |
| NGS technology is able to detect multiple splice sites and novel isoforms. | Microarray technologies cannot detect multiple splice sites and novel isoforms. |
| NGS technology is able to do de novo analysis of sample without reference genome. | Reference genome is required for the analysis of sample. |
| Disadvantages | |
| NGS based techniques are very expensive. | Microarrays are cheaper in comparison to NGS. |
| Accuracy and longevity of this approach remains questionable. | Microarray is more reliable methods in long run. |
| Low yield of high-quality sequences are obtained using NGS techniques. | Comparatively high yield of high-quality sequences is obtained using microarray technologies. |
| NGS technologies have a drawback of generating shorter sequences with more noise. | Microarray offers lesser errors and is more accurate. |
| NGS assembly algorithms show poor performance in presence of identical repeats. | Homologous repeats are identified using microarray technologies. |
| Annotation is challenging when considering complex genomes with higher repeat and duplication content. | Microarray technologies are more successful when considering complex genomes with higher repeat and duplication content. |