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Medicare Administrative Contractors (MACs) may determine coverage of diagnostic lab tests using NGS for RNA sequencing and protein analysis. Next generation sequencing (NGS), or massively parallel high-throughput sequencing, enables sequence profiling of everything from genomes and transcriptomes. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. This National Coverage Determination (NCD) is only applicable to diagnostic lab tests using NGS for somatic (acquired) and germline (inherited) cancer. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. The NGS technology uses second-generation DNA sequencing, where users perform sequencing of many samples at the same time, also known as massive parallel. And nowhere has that need been more evident than in the field of next-generation sequencing. Thus, MiSeq provides an ideal platform for rapid turnaround time. More data create more opportunities and a more pressing need for systematic methods of analysis. Next generation sequencing (NGS) data is extremely high throughput, allowing for exponentially higher amounts of data to be generated than the traditional. Combined with other technologies such as RNA extraction (RNA-Seq), enrichment for exome (Exome-seq) or other. Next-generation sequencing (NGS) is an emerging technology to determine DNA/RNA sequences for whole genome or specific regions of interest at much lower cost than traditional Sanger sequencing. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Next-Generation Sequencing Data Analysis. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. Next I plan to explore, in depth, what goes into the analysis of sequence data and why both the cost and complexity of the bioinformatics should not be ignored.