sequencingplatforms

Sequencing platforms are technologies used to determine the order of nucleotides in DNA or RNA. They differ in chemistry, read length, throughput, accuracy, and cost, and are chosen to suit specific research goals, budgets, and sample types. The earliest widely used method is Sanger sequencing, which relies on chain-terminating nucleotides and capillary electrophoresis. It provides high accuracy for individual reads but is low throughput and expensive for large genomes.

Following Sanger, most current sequencing work uses next-generation sequencing platforms that deliver massive parallelism. Illumina sequencing by synthesis is the dominant short-read technology, generating many millions of reads per run with typical lengths of 150–300 base pairs and very high per-base accuracy. It is widely used for whole-genome resequencing, exome sequencing, RNA sequencing, and targeted panels, especially when high throughput and low cost per base are priorities.

Other platforms in the short-read family include Ion Torrent, which uses semiconductor sequencing to detect nucleotide incorporation and offers faster run times with reasonable throughput, though it can struggle with homopolymers. Roche 454, once a major long-read option, has been discontinued.

Long-read sequencing technologies aim to overcome limitations of short reads for de novo assembly and structural variation detection. Pacific Biosciences has single-molecule real-time (SMRT) sequencing, delivering long reads that facilitate assembly and phasing, with accuracy improved through circular consensus sequencing. Oxford Nanopore Technologies provides nanopore sequencing with ultra-long reads and portable devices; data are produced in real time, and ongoing improvements have narrowed accuracy gaps while enabling flexible deployment.

Output from sequencing runs is typically in FASTQ or FASTA formats, followed by bioinformatic processing for alignment, variant calling, and assembly. Platform choice depends on the balance of read length, accuracy, throughput, cost, and project requirements.