Editing DNA sequencer

{{Short description|A scientific instrument used to automate the DNA sequencing process}}
{{infobox chemical analysis
| name           = DNA sequencer
| image          = DNA-Sequencers from Flickr 57080968.jpg
| caption        = DNA sequencers
| acronym        = 
| classification = 
| analytes       = 
| manufacturers  = [[Roche Applied Science|Roche]], [[Illumina (company)|Illumina]], [[Life Technologies (Thermo Fisher Scientific)|Life Technologies]], [[Beckman Coulter]], [[Pacific Biosciences]], [[BGI Group|MGI/BGI]], [[Oxford Nanopore Technologies]]
| related        = 
| hyphenated     = 
}}

A '''DNA sequencer''' is a [[scientific instrument]] used to automate the [[DNA sequencing]] process.  Given a sample of [[DNA]], a DNA sequencer is used to determine the order of the four bases: G ([[guanine]]), C ([[cytosine]]), A ([[adenine]]) and T ([[thymine]]). This is then reported as a text [[String (computer science)|string]], called a read. Some DNA sequencers can be also considered [[optical instrument]]s as they analyze light signals originating from [[fluorochrome]]s attached to [[nucleotides]].

The first automated DNA sequencer, invented by [[Lloyd M. Smith]], was introduced by [[Applied Biosystems]] in 1987.<ref>{{cite journal|last1=Cook-Deegan|first1=Robert Mullan|title=Origins of the Human Genome Project|journal=FASEB Journal|year=1991|volume=5|issue=1|pages=8–11|url=http://faculty.washington.edu/mccurdy/Project.doc|publisher=University of Washington|doi=10.1096/fasebj.5.1.1991595|doi-access=free |pmid=1991595|s2cid=37792736|access-date=20 October 2014}}</ref> It used the [[Sanger sequencing]] method, a technology which formed the basis of the "first generation" of DNA sequencers<ref name=Metzker>{{cite journal |author=Metzker, M. L. |title=Emerging technologies in DNA sequencing |journal=Genome Res. |volume=15 |issue=12 |pages=1767–1776 |year=2005 |pmid=16339375 |doi= 10.1101/gr.3770505|doi-access=free }}</ref><ref name="Hutchison, C. A. III. 2007 6227–6237">{{cite journal |author=Hutchison, C. A. III. |title=DNA sequencing: bench to bedside and beyond |journal=Nucleic Acids Res. |volume=35 |issue=18 |pages=6227–6237 |year=2007 |pmid=17855400 |doi= 10.1093/nar/gkm688 |pmc=2094077}}</ref> and enabled the completion of the [[human genome project]] in 2001.<ref name="F. S. Collins, M. Morgan, and A. Patrinos 2003 286–290">{{cite journal |author1=F. S. Collins |author2=M. Morgan |author3=A. Patrinos |title=The Human Genome Project: lessons from large-scale biology |journal=Science |volume=300 |issue=5617 |pages=286–290 |year=2003 |pmid=12690187 |doi= 10.1126/science.1084564|bibcode=2003Sci...300..286C |s2cid=22423746 |url=https://zenodo.org/record/1230828 }}</ref> This first generation of DNA sequencers are essentially automated [[electrophoresis]] systems that detect the migration of labelled DNA fragments. Therefore, these sequencers can also be used in the [[genotyping]] of genetic markers where only the length of a DNA fragment(s) needs to be determined (e.g. [[microsatellite]]s, [[Amplified fragment length polymorphism|AFLPs]]).

The [[Human Genome Project]] spurred the development of cheaper, high throughput and more accurate platforms known as [[Next-generation sequencing|Next Generation Sequencers]] (NGS) to sequence the [[human genome]]. These include the 454, [[ABI Solid Sequencing|SOLiD]] and [[Illumina (company)|Illumina]] DNA sequencing platforms. Next generation sequencing machines have increased the rate of DNA sequencing substantially, as compared with the previous Sanger methods. DNA samples can be prepared automatically in as little as 90 mins,<ref name="a tale of three" /> while a human genome can be sequenced at 15 times coverage in a matter of days.<ref name="large genome centre">{{cite journal |author1=Michael A. Quail |author2=Iwanka Kozarewa |author3=Frances Smith |author4=Aylwyn Scally |author5=Philip J. Stephens |author6=Richard Durbin |author7=Harold Swerdlow |author8=Daniel J. Turner |title=A large genome centre's improvements to the Illumina sequencing system |journal=Nat Methods |volume=5 |issue=12 |pages=1005–1010 |year=2008 |pmc=2610436 |doi=10.1038/nmeth.1270 |pmid=19034268}}</ref>

More recent, third-generation DNA sequencers such as PacBio [[Single Molecule Real Time Sequencing|SMRT]] and [[Nanopore sequencing|Oxford Nanopore]] offer the possibility of sequencing long molecules, compared to short-read technologies such as Illumina SBS or MGI Tech's DNBSEQ.

Because of limitations in DNA sequencer technology, the reads of many of these technologies are short, compared to the length of a [[genome]] therefore the reads must be [[Sequence assembly|assembled]] into longer [[contig]]s.<ref>{{Cite journal |last1=Li |first1=Heng |last2=Ruan |first2=Jue |last3=Durbin |first3=Richard |date=2008-11-01 |title=Mapping short DNA sequencing reads and calling variants using mapping quality scores |url=https://genome.cshlp.org/content/18/11/1851 |journal=Genome Research |language=en |volume=18 |issue=11 |pages=1851–1858 |doi=10.1101/gr.078212.108 |issn=1088-9051 |pmc=2577856 |pmid=18714091}}</ref> The data may also contain errors, caused by limitations in the DNA sequencing technique or by errors during [[PCR amplification]]. DNA sequencer manufacturers use a number of different methods to detect which DNA bases are present. The specific protocols applied in different sequencing platforms have an impact in the final data that is generated. Therefore, comparing data quality and cost across different technologies can be a daunting task. Each manufacturer provides their own ways to inform sequencing errors and scores. However, errors and scores between different platforms cannot always be compared directly. Since these systems rely on different DNA sequencing approaches, choosing the best DNA sequencer and method will typically depend on the experiment objectives and available budget.<ref name="Metzker"/>

==History==

The first [[DNA sequencing]] methods were developed by Gilbert (1973)<ref name="Gilbert 1973">{{cite journal |vauthors=Gilbert W, Maxam A |title=The Nucleotide Sequence of the lac Operator |journal=Proc Natl Acad Sci U S A |volume=70 |issue=12 |pages=13581–3584 |year=1973 |pmc=427284 |pmid=4587255 |doi=10.1073/pnas.70.12.3581|bibcode=1973PNAS...70.3581G |doi-access=free }}</ref> and Sanger (1975).<ref name=Sanger75>{{cite journal |vauthors=Sanger F, Coulson AR |title=A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase |journal=J. Mol. Biol. |volume=94 |issue=3 |pages=441–8 |date=May 1975 |pmid=1100841 |doi=10.1016/0022-2836(75)90213-2 }}</ref> Gilbert introduced a sequencing method based on chemical modification of DNA followed by cleavage at specific bases whereas Sanger's technique is based on [[dideoxynucleotide]] chain termination. The Sanger method became popular due to its increased efficiency and low radioactivity. The first automated DNA sequencer was the AB370A, introduced in 1986 by [[Applied Biosystems]]. The AB370A was able to sequence 96 samples simultaneously, 500 kilobases per day, and reaching read lengths up to 600 bases. This was the beginning of the "first generation" of DNA sequencers,<ref name="Metzker"/><ref name="Hutchison, C. A. III. 2007 6227–6237"/> which implemented Sanger sequencing, fluorescent dideoxy nucleotides and polyacrylamide gel sandwiched between glass plates - slab gels. The next major advance was the release in 1995 of the AB310 which utilized a linear polymer in a capillary in place of the slab gel for DNA strand separation by electrophoresis. These techniques formed the base for the completion of the human genome project in 2001.<ref name="F. S. Collins, M. Morgan, and A. Patrinos 2003 286–290"/> The human genome project spurred the development of cheaper, high throughput and more accurate platforms known as Next Generation Sequencers (NGS). In 2005, [[454 Life Sciences]] released the 454 sequencer, followed by Solexa Genome Analyzer and SOLiD (Supported Oligo Ligation Detection) by Agencourt in 2006. Applied Biosystems acquired Agencourt in 2006, and in 2007, [[Hoffmann-La Roche|Roche]] bought 454 Life Sciences, while Illumina purchased Solexa. Ion Torrent entered the market in 2010 and was acquired by Life Technologies (now [[Thermo Fisher Scientific]]). And [[BGI Group|BGI]] started manufacturing sequencers in China after acquiring [[Complete Genomics]] under their [[BGI Group|MGI]] arm. These are still the most common NGS systems due to their competitive cost, accuracy, and performance.

More recently, a third generation of DNA sequencers was introduced. The sequencing methods applied by these sequencers do not require DNA amplification (polymerase chain reaction – PCR), which speeds up the sample preparation before sequencing and reduces errors. In addition, sequencing data is collected from the reactions caused by the addition of nucleotides in the complementary strand in real time. Two companies introduced different approaches in their third-generation sequencers. [[Pacific Biosciences]] sequencers utilize a method called Single-molecule real-time (SMRT), where sequencing data is produced by light (captured by a camera) emitted when a nucleotide is added to the complementary strand by enzymes containing fluorescent dyes. [[Oxford Nanopore Technologies]] is another company developing third-generation sequencers using electronic systems based on nanopore sensing technologies.

==Manufacturers of DNA sequencers==

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.<ref name="Comparison Next-Gen Seq">{{cite journal |author1=Lin Liu |author2=Yinhu Li |author3=Siliang Li |author4=Ni Hu |author5=Yimin He |author6=Ray Pong |author7=Danni Lin |author8=Lihua Lu |author9=Maggie Law |title = Comparison of Next-Generation Sequencing Systems|journal = Journal of Biomedicine and Biotechnology|year=2012 |volume = 2012|pages = 251364|pmid = 22829749|doi = 10.1155/2012/251364|pmc=3398667 |doi-access=free }}</ref> 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.<ref>{{Cite web |url=http://454.com/products/index.asp |title=Products : 454 Life Sciences, a Roche Company<!-- Bot generated title --> |access-date=2012-09-05 |archive-url=https://web.archive.org/web/20120913054317/http://454.com/products/index.asp |archive-date=2012-09-13 |url-status=dead }}</ref> The GS FLX+ System promises read lengths of approximately 1000 base pairs while the GS Junior System promises 400 base pair reads.<ref>{{Cite web |url=http://454.com/products/gs-flx-system/index.asp |title=Products - GS FLX+ System : 454 Life Sciences, a Roche Company<!-- Bot generated title --> |access-date=2012-09-05 |archive-url=https://web.archive.org/web/20120905145227/http://454.com/products/gs-flx-system/index.asp |archive-date=2012-09-05 |url-status=dead }}</ref><ref>{{Cite web |url=http://454.com/products/gs-junior-system/index.asp |title=Products - GS Junior System : 454 Life Sciences, a Roche Company<!-- Bot generated title --> |access-date=2012-09-05 |archive-url=https://web.archive.org/web/20120913065444/http://454.com/products/gs-junior-system/index.asp |archive-date=2012-09-13 |url-status=dead }}</ref> 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.<ref>{{cite journal|last=Mardis|first=Elaine R.|s2cid=2484571|title=Next-Generation DNA Sequencing Methods|journal=Annual Review of Genomics and Human Genetics|date=1 September 2008|volume=9|issue=1|pages=387–402|doi=10.1146/annurev.genom.9.081307.164359|pmid=18576944}}</ref> 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.<ref>{{Cite web |date=2013-10-15 |title=Roche Shutting Down 454 Sequencing Business |url=https://www.genomeweb.com/sequencing/roche-shutting-down-454-sequencing-business |website=GenomeWeb |language=en}}</ref><ref>{{Cite web |last=Davies |first=Kevin |date=April 23, 2013 |title=Roche Shuts Down Third-Generation NGS Research Programs |url=https://www.bio-itworld.com/news/2013/04/23/roche-shuts-down-third-generation-ngs-research-programs |website=Pubs - Bio-IT World |language=en}}</ref>

Roche produces a number of software tools which are optimised for the analysis of 454 sequencing data.<ref name=454analysis>{{Cite web |url=http://454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp |title=Products - Analysis Software : 454 Life Science, a Roche Company |access-date=2013-10-23 |archive-url=https://web.archive.org/web/20090219223046/http://454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp |archive-date=2009-02-19 |url-status=dead }}</ref> Such as,

* ''GS Run Processor'' converts raw images generated by a sequencing run into intensity values.<ref>[http://sequence.otago.ac.nz/download/ManualPartB.pdf Genome Sequencer FLX System Software Manual, version 2.3]</ref> 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.<ref name="454analysis" /> 
* ''GS Reference Mapper'' maps short reads to a reference genome, generating a consensus sequence. The software is able to generate output files for assessment, indicating insertions, deletions and SNPs. Can handle large and complex genomes of any size.<ref name="454analysis" /> 
* Finally, the ''GS Amplicon Variant Analyzer'' aligns reads from amplicon samples against a reference, identifying variants (linked or not) and their frequencies. It can also be used to detect unknown and low-frequency variants. It includes graphical tools for analysis of alignments.<ref name="454analysis" />

===Illumina===
[[File:GA2.JPG|thumbnail|Illumina Genome Analyzer II sequencing machine]]
[[Illumina (company)|Illumina]] produces a number of next-generation sequencing machines using technology acquired from [[Manteia Predictive Medicine]] and developed by Solexa.<ref>{{cite news |last1=Marcial |first1=Gene G. |title=Solexa's Progress Is In The Genes |url=https://www.bloomberg.com/news/articles/2006-11-05/solexas-progress-is-in-the-genes |newspaper=Bloomberg |date=6 November 2006 |access-date=10 January 2022}}</ref> 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 [[DNA microarray|microarrays]].<ref>{{Cite web|url=https://www.illumina.com/systems.html|title=Sequencing and Microarray Systems|website=www.illumina.com}}</ref>

The technology leading to these DNA sequencers was first released by Solexa in 2006 as the Genome Analyzer.<ref name="Comparison Next-Gen Seq" /> Illumina purchased Solexa in 2007. The Genome Analyzer uses a sequencing by synthesis method. The first model produced 1G per run. During the year 2009 the output was increased from 20G per run in August to 50G per run in December. In 2010 Illumina released the HiSeq 2000 with an output of 200 and then 600G per run which would take 8 days. At its release the HiSeq 2000 provided one of the cheapest sequencing platforms at $0.02 per million bases as costed by the [[Beijing Genomics Institute]].

In 2011 Illumina released a benchtop sequencer called the MiSeq. At its release the MiSeq could generate 1.5G per run with paired end 150bp reads. A sequencing run can be performed in 10 hours when using automated DNA sample preparation.<ref name="Comparison Next-Gen Seq" />

The Illumina HiSeq uses two software tools to calculate the number and position of DNA clusters to assess the sequencing quality: the HiSeq control system and the real-time analyzer. These methods help to assess if nearby clusters are interfering with each other.<ref name="Comparison Next-Gen Seq" />

===Life Technologies===
[[Life Technologies (Thermo Fisher Scientific)|Life Technologies]] (now [[Thermo Fisher Scientific]]) produces DNA sequencers under the [[Applied Biosystems]] and [[Ion Torrent]] brands. Applied Biosystems makes the SOLiD next-generation sequencing platform,<ref>{{Cite web|url=https://www.thermofisher.com/us/en/home/brands/applied-biosystems.html?cid=fl-appliedbiosystems|title=Applied Biosystems - US|website=www.thermofisher.com}}</ref> and Sanger-based DNA sequencers such as the 3500 Genetic Analyzer.<ref>{{Cite web|url=https://www.thermofisher.com/us/en/home/life-science/sequencing/sanger-sequencing.html|title=Sanger Sequencing and Fragment Analysis by CE - US|website=www.thermofisher.com}}</ref> 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.<ref>{{Cite web |title=Ion Torrent |url=http://www.thermofisher.com/iontorrent}}</ref> The company is also believed to be developing their new capillary DNA sequencer called SeqStudio that will be released early 2018.<ref>{{Cite web | url=https://www.thermofisher.com/us/en/home/products-and-services/promotions/life-science/seqstudio-genetic-analyzer.html | title=Applied Biosystems SeqStudio Genetic Analyzer - US}}</ref>

SOLiD systems was acquired by [[Applied Biosystems]] in 2006. SOLiD applies sequencing by ligation and [[2 base encoding|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.<ref name="Comparison Next-Gen Seq" />

The limited read length of the SOLiD has remained a significant shortcoming<ref>{{Cite web|url=https://www.thermofisher.com/us/en/home/brands/applied-biosystems.html|title=Applied Biosystems - US|website=www.thermofisher.com}}</ref> 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.<ref name="Comparison Next-Gen Seq" /> The DNA sample preparation time for SOLiD systems has become much quicker with the automation of sequencing library preparations such as the Tecan system.<ref name="Comparison Next-Gen Seq" />

The colour space data produced by the SOLiD platform can be decoded into DNA bases for further analysis, however software that considers the original colour space information can give more accurate results. Life Technologies has released BioScope,<ref>{{Cite web|url=https://www.thermofisher.com/us/en/home/life-science/sequencing.html|title=Sequencing - US|website=www.thermofisher.com}}</ref> 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 Corporation|Danaher]]) has previously manufactured chain termination and capillary electrophoresis-based DNA sequencers under the model name CEQ, including the CEQ 8000.<ref>{{Cite book |last1=Brown |first1=Ross D. |url=https://books.google.com/books?id=s--zG1BuZSoC&dq=Beckman+Coulter+ceq+8000&pg=PA273 |title=Multiple Myeloma: Methods and Protocols |last2=Ho |first2=P. Joy |date=2008-02-01 |publisher=Springer Science & Business Media |isbn=978-1-59259-916-5 |language=en}}</ref> The company now produces the GeXP Genetic Analysis System, which uses [[dye terminator sequencing]].<ref>{{Cite web|date=August 2014|title=GenomeLab GeXP manual|url=https://scheduleit.mec.cuny.edu/wp-content/uploads/2017/12/GenomeLab-GeXP-manual.pdf|url-status=live|website=[[Medgar Evers College]], [[City University of New York]]|archive-url=https://web.archive.org/web/20211205040329/https://scheduleit.mec.cuny.edu/wp-content/uploads/2017/12/GenomeLab-GeXP-manual.pdf |archive-date=2021-12-05 }}</ref> This method uses a [[thermocycler]] in much the same way as [[Polymerase chain reaction|PCR]] to denature, anneal, and extend DNA fragments, amplifying the sequenced fragments.<ref>{{cite journal|last=Rai|first=Alex J.|author2=Kamath, Rashmi M. |author3=Gerald, William |author4= Fleisher, Martin |title=Analytical validation of the GeXP analyzer and design of a workflow for cancer-biomarker discovery using multiplexed gene-expression profiling|journal=Analytical and Bioanalytical Chemistry|date=29 October 2008|volume=393|issue=5|pages=1505–1511|doi=10.1007/s00216-008-2436-7|pmid=18958454|s2cid=46721686}}</ref><ref>[http://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/genetic-analysis-systems/genomelab-gexp-genetic-analysis-system/index.htm#overview Beckman Coulter, Inc - GenomeLab GeXP Genetic Analysis System]{{Dead link|date=March 2023}}</ref>

===Pacific Biosciences===
[[Pacific Biosciences]] produces the PacBio RS and Sequel sequencing systems using a [[single molecule real time sequencing]], or SMRT, method.<ref>{{Cite web|url=https://www.pacb.com/products-and-services/sequel-system/|title=PacBio Sequel Systems}}</ref> 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 [[Sequence assembly|assembly]] strategies.<ref>{{cite journal|last=Koren|first=S |author2=Schatz, MC |author3=Walenz, BP |author4=Martin, J |author5=Howard, JT |author6=Ganapathy, G |author7=Wang, Z |author8=Rasko, DA |author9=McCombie, WR |author10=Jarvis, ED |author11=Phillippy, AM|title=Hybrid error correction and de novo assembly of single-molecule sequencing reads.|journal=Nature Biotechnology|date=Jul 1, 2012|pmid=22750884|pmc=3707490 |doi=10.1038/nbt.2280|volume=30|issue=7|pages=693–700}}</ref> Scientists have reported 99.9999% accuracy with these strategies.<ref>{{Cite journal | doi=10.1038/nmeth.2474| title=Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data| year=2013| last1=Chin| first1=Chen-Shan| last2=Alexander| first2=David H.| last3=Marks| first3=Patrick| last4=Klammer| first4=Aaron A.| last5=Drake| first5=James| last6=Heiner| first6=Cheryl| last7=Clum| first7=Alicia| last8=Copeland| first8=Alex| last9=Huddleston| first9=John| last10=Eichler| first10=Evan E.| last11=Turner| first11=Stephen W.| last12=Korlach| first12=Jonas| journal=Nature Methods| volume=10| issue=6| pages=563–569| pmid=23644548| s2cid=205421576}}</ref> The Sequel system was launched in 2015 with an increased capacity and a lower price.<ref>{{Cite web |last=Krol |first=Aaron |date=October 1, 2015 |title=A Worthy Sequel: PacBio's New Sequencing System |url=http://www.bio-itworld.com/2015/10/1/a-worthy-sequel.aspx}}</ref><ref>{{Cite web | url=https://www.genomeweb.com/business-news/pacbio-launches-higher-throughput-lower-cost-single-molecule-sequencing-system |title = PacBio Launches Higher-Throughput, Lower-Cost Single-Molecule Sequencing System|date = October 2015}}</ref>

[[File:First-ever sequencing of DNA in space, performed by Kate Rubins on the ISS. 128f0462 sequencer 1.jpg|thumb|Oxford Nanopore MinION sequencer (lower right) was used in the first-ever DNA sequencing in space in August 2016 by astronaut [[Kathleen Rubins]].<ref>{{cite web|url=http://www.nasa.gov/mission_pages/station/research/news/dna_sequencing|title=First DNA Sequencing in Space a Game Changer|last=Gaskill|first=Melissa|work=NASA|date=August 29, 2016|access-date=October 26, 2016}}</ref>]]

=== Oxford Nanopore ===
[[Oxford Nanopore Technologies]]' MinION sequencer is based on evolving [[nanopore sequencing]] technology to nucleic acid analyses.<ref>{{Cite journal|last1=Tyler|first1=Andrea D.|last2=Mataseje|first2=Laura|last3=Urfano|first3=Chantel J.|last4=Schmidt|first4=Lisa|last5=Antonation|first5=Kym S.|last6=Mulvey|first6=Michael R.|last7=Corbett|first7=Cindi R.|date=2018-07-19|title=Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications|journal=Scientific Reports|language=en|volume=8|issue=1|pages=10931|doi=10.1038/s41598-018-29334-5|pmid=30026559|pmc=6053456|bibcode=2018NatSR...810931T|issn=2045-2322}}</ref> 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.<ref>{{Cite journal|last1=Jain|first1=Miten|last2=Koren|first2=Sergey|last3=Miga|first3=Karen H.|author-link3=Karen Miga|last4=Quick|first4=Josh|last5=Rand|first5=Arthur C.|last6=Sasani|first6=Thomas A.|last7=Tyson|first7=John R.|last8=Beggs|first8=Andrew D.|last9=Dilthey|first9=Alexander T.|last10=Fiddes|first10=Ian T.|last11=Malla|first11=Sunir|date=29 January 2018|title=Nanopore sequencing and assembly of a human genome with ultra-long reads|journal=Nature Biotechnology|language=en|volume=36|issue=4|pages=338–345|doi=10.1038/nbt.4060|pmid=29431738|pmc=5889714|issn=1546-1696}}</ref> 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.<ref>{{Cite web|title=MinION USB-sized DNA sequencer goes through real-world testing|url=https://www.engadget.com/2014-09-18-minion-usb-dna-sequencer-beta-test.html|access-date=2021-12-05|website=Engadget|date=19 September 2014 |language=en-US}}</ref> Even inaccurate results may prove useful because it produces long read lengths.<ref>{{Cite journal|last1=Lu|first1=Hengyun|last2=Giordano|first2=Francesca|last3=Ning|first3=Zemin|date=2016-10-01|title=Oxford Nanopore MinION Sequencing and Genome Assembly|journal=Genomics, Proteomics & Bioinformatics|series=SI: Big Data and Precision Medicine|language=en|volume=14|issue=5|pages=265–279|doi=10.1016/j.gpb.2016.05.004|pmid=27646134|pmc=5093776|issn=1672-0229}}</ref> 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.<ref>{{Cite web|title=New method helps pocket-sized DNA sequencer achieve near-perfect accuracy|url=https://www.sciencedaily.com/releases/2021/01/210112144811.htm|access-date=2021-12-05|website=ScienceDaily|language=en}}</ref> 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.<ref>{{Cite news|url = http://www.technologyreview.com/news/530746/radical-new-dna-sequencer-finally-gets-into-researchers-hands|title = Radical New DNA Sequencer Finally Gets into Researchers' Hands|last = Regalado|first = Antonio|date = September 17, 2014|work = Technology Review|access-date = October 3, 2014}}</ref>

=== MGI ===
[[MGI (company)|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.<ref>{{Cite web|last1=LeMieux|first1=Julianna|last2=PhD|date=2020-12-03|title=Genomics Analysis Moves to the Next Level|url=https://www.genengnews.com/insights/genomics-analysis-moves-to-the-next-level/|access-date=2021-12-20|website=GEN - Genetic Engineering and Biotechnology News|language=en-US}}</ref> 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 [[Nucleic acid hybridization|hybridization]]. DNBSEQ-T7 can generate short reads at a very large scale—up to 60 human genomes per day.<ref>{{Cite journal|last1=Kim|first1=Hak-Min|last2=Jeon|first2=Sungwon|last3=Chung|first3=Oksung|last4=Jun|first4=Je Hoon|last5=Kim|first5=Hui-Su|last6=Blazyte|first6=Asta|last7=Lee|first7=Hwang-Yeol|last8=Yu|first8=Youngseok|last9=Cho|first9=Yun Sung|last10=Bolser|first10=Dan M|last11=Bhak|first11=Jong|date=2021-03-01|title=Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing|url=https://doi.org/10.1093/gigascience/giab014|journal=GigaScience|volume=10|issue=3|pages=giab014|doi=10.1093/gigascience/giab014|pmid=33710328|pmc=7953489|issn=2047-217X}}</ref> 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.<ref>{{Cite journal|last1=C Anukam|first1=Kingsley|last2=E Bassey|first2=Bassey|year=2020|title=Genetic Variants predisposition to Severe COVID-19 Illness Identified in a Healthy Nigerian Man, using Nebula Genomics Gene.iobio Platform|url=http://www.jomls.org/en/publications/acceptedpapers/vol30no4/Anukam_and_Bassey.pdf|journal=Journal of Medical Laboratory Science|volume=30|issue=4|pages=62–75|doi=10.5281/zenodo.4399050|s2cid=244988198 |issn=1116-1043}}</ref> Using a novel technique the researchers from [[China National GeneBank]] sequenced [[polymerase chain reaction|PCR]]-free libraries on MGI's PCR-free DNBSEQ arrays to obtain for the first time a true PCR-free [[whole genome sequencing]].<ref>{{cite bioRxiv |last1=Shen |first1=Hanjie |last2=Liu |first2=Pengjuan |last3=Li |first3=Zhanqing |last4=Chen |first4=Fang |last5=Jiang |first5=Hui |last6=Shi |first6=Shiming |last7=Xi |first7=Yang |last8=Li |first8=Qiaoling |last9=Wang |first9=Xiaojue |last10=Zhao |first10=Jing |last11=Liang |first11=Xinming |last12=Xie |first12=Yinlong |last13=Wang |first13=Lin |last14=Tian |first14=Wenlan |last15=Berntsen |first15=Tam |last16=Alexeev |first16=Andrei |last17=Luo |first17=Yinling |last18=Gong |first18=Meihua |last19=Li |first19=Jiguang |last20=Xu |first20=Chongjun |last21=Barua |first21=Nina |last22=Drmanac |first22=Snezana |last23=Dai |first23=Sijie |last24=Mi |first24=Zilan |last25=Ren |first25=Han |last26=Lin |first26=Zhe |last27=Chen |first27=Ao |last28=Zhang |first28=Wenwei |last29=Mu |first29=Feng |last30=Xu |first30=Xun |last31=Zhao |first31=Xia |last32=Jiang |first32=Yuan |last33=Drmanac |first33=Radoje |title=Advanced Whole Genome Sequencing Using an Entirely PCR-free Massively Parallel Sequencing Workflow |date=23 December 2019 |biorxiv=10.1101/2019.12.20.885517}}</ref> 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]].<ref>{{Cite journal|last1=Liao|first1=Mingfeng|last2=Liu|first2=Yang|last3=Yuan|first3=Jing|last4=Wen|first4=Yanling|last5=Xu|first5=Gang|last6=Zhao|first6=Juanjuan|last7=Cheng|first7=Lin|last8=Li|first8=Jinxiu|last9=Wang|first9=Xin|last10=Wang|first10=Fuxiang|last11=Liu|first11=Lei|date=May 12, 2020|title=Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19|journal=Nature Medicine|language=en|volume=26|issue=6|pages=842–844|doi=10.1038/s41591-020-0901-9|pmid=32398875|s2cid=218593518|issn=1546-170X|doi-access=free}}</ref>

==Comparison==
[[List of DNA sequencers|Current offerings in DNA sequencing technology]] show a dominant player: [[Illumina, Inc.|Illumina]] (December 2019), followed by [[Pacific Biosciences|PacBio]], [[BGI Group|MGI]] and [[Oxford Nanopore Technologies|Oxford Nanopore]].
{| class="wikitable"
|+ Comparing metrics and performance of next-generation DNA sequencers.<ref name="shendure">{{cite journal | last1 = Shendure | first1 = J. | last2 = Ji | first2 = H.  | year = 2008 | title = Next-generation DNA sequencing | journal = Nat. Biotechnol. | volume = 26 | issue = 10| pages = 1135–1145 | doi=10.1038/nbt1486 | pmid=18846087| s2cid = 6384349 }}</ref>
|-
! Sequencer
! '''Ion Torrent PGM'''<ref name="a tale of three">{{Cite journal |last1=Quail |first1=Michael A. |last2=Smith |first2=Miriam |last3=Coupland |first3=Paul |last4=Otto |first4=Thomas D. |last5=Harris |first5=Simon R. |last6=Connor |first6=Thomas R. |last7=Bertoni |first7=Anna |last8=Swerdlow |first8=Harold P. |last9=Gu |first9=Yong |date=2012-07-24 |title=A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers |journal=BMC Genomics |volume=13 |issue=1 |pages=341 |doi=10.1186/1471-2164-13-341 |pmid=22827831 |pmc=3431227 |issn=1471-2164 |doi-access=free }}</ref><ref name="karow agbt">{{Cite web |last=Karow |first=Julia |date=2010-03-02 |title=Ion Torrent Systems Presents $50,000 Electronic Sequencer at AGBT |url=https://www.genomeweb.com/sequencing/ion-torrent-systems-presents-50000-electronic-sequencer-agbt |website=GenomeWeb |language=en}}</ref><ref name=PGM>{{Cite web |url=http://www.iontorrent.com/products-ion-pgm/ |title=Ion PGM - Ion Torrent<!-- Bot generated title --> |access-date=2013-02-13 |archive-url=https://web.archive.org/web/20120920083447/http://www.iontorrent.com/products-ion-pgm |archive-date=2012-09-20 |url-status=dead }}</ref>
! '''454 GS FLX'''<ref name="Comparison Next-Gen Seq" />
! '''HiSeq 2000'''<ref name="a tale of three"/><ref name="Comparison Next-Gen Seq" />
! '''SOLiDv4'''<ref name="Comparison Next-Gen Seq" />
! '''PacBio'''<ref name="a tale of three"/><ref name=PacBio>{{Cite web|url=https://www.pacb.com/|title=Home - PacBio - Sequence with Confidence|website=PacBio}}</ref>
! '''Sanger 3730xl'''<ref name="Comparison Next-Gen Seq" />
! '''MGI DNBSEQ-G400'''<ref name="biorxiv-DNBSEQ-G400">{{Cite bioRxiv |biorxiv=10.1101/2020.07.02.185710 |first1=Xiaohuan |last1=Sun |first2=Jingjing |last2=Wang |title=Efficient and stable metabarcoding sequencing from DNBSEQ-G400 sequencer examined by large fungal community analysis |date=2020-07-03 |language=en |last3=Fang |first3=Chao |last4=Li |first4=Jiguang |last5=Han |first5=Mo |last6=Wei |first6=Xiaofang |last7=Zheng |first7=Haotian |last8=Luo |first8=Xiaoqing |last9=Gong |first9=Meihua |last10=Xiao |first10=Liang |last11=Hu |first11=Yuehua |last12=Song |first12=Zewei}}</ref>
|-
| Manufacturer
| Ion Torrent (Life Technologies)
| 454 Life Sciences (Roche)
| Illumina
| Applied Biosystems (Life Technologies)
| Pacific Biosciences
| Applied Biosystems (Life Technologies)
| MGI
|-
| Sequencing Chemistry
| Ion semiconductor sequencing
| [[Pyrosequencing]]
| Polymerase-based sequence-by-synthesis
| [[Sequencing by ligation|Ligation-based sequencing]]
| Phospholinked fluorescent nucleotides
| Dideoxy chain termination
| Polymerase-based sequence-by-synthesis
|-
| Amplification approach
| Emulsion PCR
| Emulsion PCR
| Bridge amplification
| Emulsion PCR
| Single-molecule; no amplification
| PCR
| DNA nanoball (DNB) generation
|-
| Data output per run
| 100-200 Mb
| 0.7 Gb
| 600 Gb
| 120 Gb
| 0.5 - 1.0 Gb
| 1.9~84 Kb
| 1440 Gb / 1500-1800M reads
|-
| Accuracy
| 99%
| 99.9%
| 99.9%
| 99.94%
| 88.0% (>99.9999% CCS or HGAP)
| 99.999%
| 99.90%
|-
| Time per run
| 2 hours
| 24 hours
| 3–10 days
| 7–14 days
| 2–4 hours
| 20 minutes - 3 hours
| 3–5 days
|-
| Read length
| 200-400 bp
| 700 bp
| 100x100 bp paired end
| 50x50 bp paired end
| 14,000 bp ([[N50 statistic|N50]])
| 400-900 bp
| 100/150/200 bp paired end
|-
| Cost per run
| US$350
| US$7,000
| US$6,000 (30x human genome)
| US$4,000
| $125–300 USD
| US$4 (single read/reaction)
| N/A
|-
| Cost per Mb
| US$1.00
| US$10
| US$0.07
| US$0.13
| $0.13 - US$0.60
| US$2400
| $0.007
|-
| Cost per instrument
| US$80,000
| US$500,000
| US$690,000
| US$495,000
| US$695,000
| US$95,000
| N/A
|}

==References==
{{Reflist|35em}}

{{DEFAULTSORT:Dna sequencer}}
[[Category:DNA sequencing]]
[[Category:Genetics techniques]]
[[Category:Molecular biology laboratory equipment]]
[[Category:Scientific instruments]]