DNA sequencers have been developed, manufactured, and sold by the following companies, among others.
Roche The 454 DNA sequencer was the first next-generation sequencer to become commercially successful. It was developed by
454 Life Sciences and purchased by
Roche in 2007. 454 utilizes the detection of
pyrophosphate released by the
DNA polymerase reaction when adding a nucleotide to the template strain. Roche currently manufactures two systems based on their pyrosequencing technology: the GS FLX+ and the GS Junior System. The GS FLX+ System promises read lengths of approximately 1000 base pairs while the GS Junior System promises 400 base pair reads. A predecessor to GS FLX+, the 454 GS FLX Titanium system was released in 2008, achieving an output of 0.7G of data per run, with 99.9% accuracy after quality filter, and a read length of up to 700bp. In 2009, Roche launched the GS Junior, a bench top version of the 454 sequencer with read length up to 400bp, and simplified library preparation and data processing. One of the advantages of 454 systems is their running speed. Manpower can be reduced with automation of library preparation and semi-automation of emulsion PCR. A disadvantage of the 454 system is that it is prone to errors when estimating the number of bases in a long string of identical nucleotides. This is referred to as a homopolymer error and occurs when there are 6 or more identical bases in row. Another disadvantage is that the price of reagents is relatively more expensive compared with other next-generation sequencers. In 2013 Roche announced that they would be shutting down development of 454 technology and phasing out 454 machines completely in 2016 when its technology became noncompetitive. Roche produces a number of software tools which are optimised for the analysis of 454 sequencing data. Such as, •
GS Run Processor converts raw images generated by a sequencing run into intensity values. The process consists of two main steps: image processing and signal processing. The software also applies normalization, signal correction, base-calling and quality scores for individual reads. The software outputs data in Standard Flowgram Format (or SFF) files to be used in data analysis applications (GS De Novo Assembler, GS Reference Mapper or GS Amplicon Variant Analyzer). •
GS De Novo Assembler is a tool for
de novo assembly of whole-genomes up to 3GB in size from shotgun reads alone or combined with paired end data generated by 454 sequencers. It also supports de novo assembly of transcripts (including analysis), and also isoform variant detection. Illumina makes a number of next generation sequencing machines using this technology including the HiSeq, Genome Analyzer IIx, MiSeq and the HiScanSQ, which can also process
microarrays. The technology leading to these DNA sequencers was first released by Solexa in 2006 as the Genome Analyzer. and Sanger-based DNA sequencers such as the 3500 Genetic Analyzer. Under the Ion Torrent brand, Applied Biosystems produces four next-generation sequencers: the Ion PGM System, Ion Proton System, Ion S5 and Ion S5xl systems. The company is also believed to be developing their new capillary DNA sequencer called SeqStudio that will be released early 2018. SOLiD systems was acquired by
Applied Biosystems in 2006. SOLiD applies sequencing by ligation and
dual base encoding. The first SOLiD system was launched in 2007, generating reading lengths of 35bp and 3G data per run. After five upgrades, the 5500xl sequencing system was released in 2010, considerably increasing read length to 85bp, improving accuracy up to 99.99% and producing 30G per 7-day run. and has to some extent limited its use to experiments where read length is less vital such as resequencing and transcriptome analysis and more recently ChIP-Seq and methylation experiments. a data analysis package for resequencing, ChiP-Seq and transcriptome analysis. It uses the MaxMapper algorithm to map the colour space reads.
Beckman Coulter Beckman Coulter (now
Danaher) has previously manufactured chain termination and capillary electrophoresis-based DNA sequencers under the model name CEQ, including the CEQ 8000. The company now produces the GeXP Genetic Analysis System, which uses
dye terminator sequencing. This method uses a
thermocycler in much the same way as
PCR to denature, anneal, and extend DNA fragments, amplifying the sequenced fragments.
Pacific Biosciences Pacific Biosciences produces the PacBio RS and Sequel sequencing systems using a
single molecule real time sequencing, or SMRT, method. This system can produce read lengths of multiple thousands of base pairs. Higher raw read errors are corrected using either circular consensus - where the same strand is read over and over again - or using optimized
assembly strategies. Scientists have reported 99.9999% accuracy with these strategies. The Sequel system was launched in 2015 with an increased capacity and a lower price. .
Oxford Nanopore Oxford Nanopore Technologies' MinION sequencer is based on evolving
nanopore sequencing technology to
nucleic acid analyses. The device is four inches long and gets power from a
USB port. MinION decodes DNA directly as the molecule is drawn at the rate of 450 bases/second through a
nanopore suspended in a membrane. Changes in electric current indicate which base is present. Initially, the device was 60 to 85 percent accurate, compared with 99.9 percent in conventional machines. Even inaccurate results may prove useful because it produces long read lengths. In early 2021, researchers from
University of British Columbia has used special molecular tags and able to reduce the five-to-15 per cent error rate of the device to less than 0.005 per cent even when sequencing many long stretches of DNA at a time. There are two more product iterations based on MinION; the first one is the GridION which is a slightly larger sequencer that processes up to five MinION flow cells at once. And, the second one is the PromethION which uses as many as 100,000 pores in parallel, more suitable for high volume sequencing.
MGI MGI produces high-throughput sequencers for scientific research and clinical applications such as DNBSEQ-G50, DNBSEQ-G400, and DNBSEQ-T7, under a proprietary DNBSEQ technology. It is based upon
DNA nanoball sequencing and combinatorial probe anchor synthesis technologies, in which DNA nanoballs (DNBs) are loaded onto a patterned array chip via the fluidic system, and later a sequencing primer is added to the adaptor region of DNBs for
hybridization. DNBSEQ-T7 can generate short reads at a very large scale—up to 60 human genomes per day. DNBSEQ-T7 was used to generate 150 bp paired-end reads, sequencing 30X, to sequence the genome of SARS-CoV-2 or COVID-19 to identify the genetic variants predisposition in severe COVID-19 illness. Using a novel technique the researchers from
China National GeneBank sequenced
PCR-free libraries on MGI's PCR-free DNBSEQ arrays to obtain for the first time a true PCR-free
whole genome sequencing. MGISEQ-2000 was used in single-cell RNA sequencing to study the underlying pathogenesis and recovery in COVID-19 patients, as published in
Nature Medicine. ==Comparison==