![]() This continued re-assessment is of particular importance as researchers adapt both of these sequencing platforms for use in the clinical setting. With the rapid pace of development in these sequencing technologies, we must continue to compare these two platforms in order to maintain an accurate understanding of their relative performances. These studies provide a basic indication of the error rates and reproducibility these platforms achieve, however there are two motivations for performing the present analysis.įirst, in the intervening years both Illumina and Ion Torrent have released platform updates in the form of improved sequencing chemistry, nucleotide detection, and throughput. ![]() Prior studies have compared these two sequencing platforms for various applications including genome sequencing, RNA-Seq, and microbiome profiling. Additionally, the current generation of Illumina instruments can generate sequence reads from both ends of a fragment (“paired-end” reads), while Ion Torrent cannot. In Illumina data all sequence reads generated during a single experiment have the same lengths, while the lengths of Ion Torrent reads vary. In addition to the distinct sequencing technologies used by these two platforms, there are smaller differences in the types of data they generate. One alternative option is provided by Ion Torrent, which is built around the use of pH measurements to read nucleotide sequences. Currently, the most commonly used sequencing platforms are provided by Illumina, which uses a fluorescence-based paradigm for reading the bases in a nucleotide sequence. RNA-Sequencing (RNA-Seq) broadly refers to a family of experimental techniques that give researchers the ability to study the transcriptional landscapes of cells and tissues quantitatively by exploiting high throughput sequencing technology. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features for example, disentangling the source of expression in gene-pseudogene pairs. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. ![]() Here we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments.
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