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Introduction to Illumina Sequencing By Synthesis (SBS) Next Generation Sequencing Technology

Illumina, Inc. (San Diego, California) is the most widely-used and successful NGS technology provider worldwide. The NGS technology market share is estimated to be 71% (Google). Illumina uses a technology based on a flow cell where millions of target sequences are sequenced in parallel by bridge amplification and sequencing by synthesis (SBS) technology.
In terms of cost per sequenced nucleotide Illumina is the most reasonable technology. This is due to the high sequencing throughput per run.

Illumina Sequencing Technology and Sequencing Read Length

Illumina sequencing instruments and reagents support massively parallel sequencing using a proprietary method to detect single bases as they are incorporated into growing DNA strands. The technology enables single read and paired end libraries, with a read length varying between 100 and 650 (paired end sequencing) nucleotides. The chemistry, sequencing platform, and used protocol influences the read length. Illumina indicates read length from 2x 150 to 2x 300 nucleotides for paired end sequencing. The 2x 300 nucleotide read length is currently only implemented in the MiSeq series. The following video demonstrates in more detail how the sequencing by synthesis (SBS) technology works.

Sequencing Time and Sequencing Throughput

Depending on the sequencing system and desired read length the sequencing time can take up to six days to complete one run. The lately (early 2016) launched MiniSeq system enables the fastest sequencing results within 4 to 24 hours, whereas maximal read length will be achieved after 24 hours.
The number of reads per run can vary from 25 million reads (MiSeq and MiniSeq) up to 6 billion reads with the HiSeq X series.

Illumina Sequencing Platforms and its Applications

In January 2016 Illumina launched the MiniSeq sequencer. The MiniSeq offers an intuitive user interface as well as load-and-go operation. The sequencing run takes less than one day. The system integrates sequencing and data analysis in one single instrument. This system is especially designed for targeted RNA and DNA sequencing in human genetics and diagnostics such as cancer screening or human inheritability testing.
The MiSeq series is mainly developed for targeted and sequencing of small genomes such as viral genomes, for application in forensic (MiSeq FGx) and for application in molecular diagnostics such as bacterial identification (MiSeq Dx).
The NextSeq system has a maximal data output of 120Gb and is especially developed for exome, transcriptome and targeted resequencing projects.
For high throughput sequencing such as human, plant or animal whole genome sequencing the Illumina HiSeq and HiSeq X series are the best suitable platforms as they enable massive sequencing data output.
For more detailed information on the different platforms and its applications visit the Illumina website.