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Choosing the Right NGS Sequencing Instrument for Your Study

⬅️ NGS Handbook

The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you’re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our free consultation form and we'll get in touch with you to help.

Apart from some minor considerations Genohub's NGS Matching Engine makes it very easy to see what instruments fit your project best. Simply enter your specifications and instantly see services that match your output requirements.

Table 1: Comparison of all NGS Instruments

Platform	Instrument	Unit	Reads/Unit*	Max Read Length	Read Type	Error Type	Highlight	Reference
Illumina	GAIIx	Lane	37,500,000	1x35bp to 2x150bp	SR & PE	Substitution	Higher per bp cost than HiSeq, no future development planned by Illumina. Discontinued in 2014.	Reference
Illumina	HiScanSQ	Lane	93,750,000	1x35bp to 2x100bp	SR & PE	Substitution	Versatility to scan microarray and sequence on the same instrument, output slightly less than HiSeq. Discontinued by Illumina in 2014.	Reference
Illumina	HiSeq 3000/4000	Lane	312,500,000	1x50bp to 2x150bp	SR & PE	Substitution	Takes advantage of patterned flow cell technology to get more reads/lane. The HiSeq 3000 has an output of 750 Gb or 2.5B PE150 reads in 3.5 days. The HiSeq 4000 has two flow cells, so twice the output: 1.5 Tb, 5B PE150 reads in 3.5 days.	Reference
Illumina	HiSeq High-Output v3	Lane	187,500,000	1x36bp to 2x125bp	SR & PE	Substitution	v3 chemistry offers fewer reads per lane compared to v4	Reference
Illumina	HiSeq High-Output v4	Lane	250,000,000	1x36bp to 2x125bp	SR & PE	Substitution	Well suited for de novo and resequencing of small and large genomes, this Illumina instrument is today's sequencing workhorse. Latest v4 chemistry now allows more reads per lane and a slightly longer read length, 2x125 bp	Reference
Illumina	HiSeq Rapid Run	Lane	150,000,000	1x36bp to 2x250bp	SR & PE	Substitution	Same as HiSeq run, except option available for faster run time, slightly less reads	Reference
Illumina	HiSeq X	Lane	375,000,000	2x150bp	PE	Substitution	Greatest throughput and number of reads compared to all other instruments previously, designed for human and non-human whole human genome sequencing.	Reference
Illumina	MiSeq	Lane	5,000,000	1x36bp to 2x250bp	SR & PE	Substitution		Reference
Illumina	MiSeq i100 - 100M	Lane	100,000,000	1x100bp to 2x150bp	SR & PE	Substitution	The MiSeq i100 offers fast and flexible sequencing for labs that run a variety of experiments and need quick data. It would fit well in smaller researcher labs that don't need the high output of a NovaSeq.	Reference
Illumina	MiSeq i100 - 25M	Lane	25,000,000	1x100bp to 2x300bp	SR & PE	Substitution	The MiSeq i100 offers fast and flexible sequencing for labs that run a variety of experiments and need quick data. It would fit well in smaller researcher labs that don't need the high output of a NovaSeq.	Reference
Illumina	MiSeq i100 - 50M	Lane	50,000,000	1x100bp to 2x300bp	SR & PE	Substitution	The MiSeq i100 offers fast and flexible sequencing for labs that run a variety of experiments and need quick data. It would fit well in smaller researcher labs that don't need the high output of a NovaSeq.	Reference
Illumina	MiSeq i100 - 5M	Lane	5,000,000	2x150bp to 2x300bp	PE	Substitution	The MiSeq i100 offers fast and flexible sequencing for labs that run a variety of experiments and need quick data. It would fit well in smaller researcher labs that don't need the high output of a NovaSeq.	Reference
Illumina	MiSeq v2	Lane	17,000,000	1x36bp to 2x250bp	SR & PE	Substitution		Reference
Illumina	MiSeq v2 Micro	Lane	4,000,000	2x150bp	PE	Substitution		Reference
Illumina	MiSeq v2 Nano	Lane	1,000,000	2x150bp to 2x250bp	PE	Substitution		Reference
Illumina	MiSeq v3	Lane	25,000,000	2x75bp to 2x300bp	PE	Substitution	Illumina's longest read instrument, the MiSeq offer 2x300 bp read lengths if v3 cluster chemistry is used. Read quality tends to drop on read 2 around 200-250 bases in, as issue Illumina is aware of.	Reference
Illumina	MiniSeq High-Output	Lane	25,000,000	1x75bp to 2x150bp	SR & PE	Substiution	Illumina's lowest output instrument, the MiniSeq, is ideal for targeted sequencing applications where a high output of reads isn't required. The instrument has an attractive $50K entry price.	Reference
Illumina	MiniSeq Mid-Output	Lane	8,000,000	2x150bp	PE	Substitution	MiniSeq has a Mid-Output mode that offers 3x fewer reads than High-Out put mode.	Reference
Illumina	MiniSeq Rapid	Lane	20,000,000	1x100	SR	Substitution		Reference
Illumina	NextSeq 1000/2000 P1	Run	100,000,000	1x300bp, 2x150bp	SR & PE	Substitution		Reference
Illumina	NextSeq 1000/2000 P2	Run	400,000,000	1x300bp, 2x150bp	SR & PE	Substitution		Reference
Illumina	NextSeq 1000/2000 P3	Run	1,200,000,000	1x300bp, 2x150bp	SR & PE	Substitution		Reference
Illumina	NextSeq 1000/2000 P4	Run	1,800,000,000	1x50bp to 2x150bp	SR & PE	Substitution		Reference
Illumina	NextSeq 500 High-Output	Run	400,000,000	1x75bp to 2x150bp	SR & PE	Substitution	Highest output of any desktop sequencer, this instrument is ideally suited for exome, transcriptomics, whole genome and targeted resequencing.	Reference
Illumina	NextSeq 500 Mid-Output	Run	130,000,000	2x75 to 2x150bp	PE	Substitution		Reference
Illumina	NextSeq 500 v2 High-Output	Run	400,000,000	1x75bp to 2x150bp	SR & PE	Substitution	Highest output of any desktop sequencer, this instrument is ideally suited for exome, transcriptomics, whole genome and targeted resequencing.	Reference
Illumina	NextSeq 500 v2 Mid-Output	Run	130,000,000	2x75 to 2x150bp	PE	Substitution		Reference
Illumina	NovaSeq - S1	Lane	800,000,000	1x300bp, 2x150bp	SR & PE	Substitution		Reference
Illumina	NovaSeq - S2	Lane	1,650,000,000	1x300bp, 2x150bp	SR & PE	Substitution		Reference
Illumina	NovaSeq - S4	Lane	2,500,000,000	1x300bp, 2x150bp	SR & PE	Substitution	Launced in January 2017, NovaSeq is Illumina's latest high-output instrument. The instrument is designed for research labs that can't afford the capital costs of the HiSeq X. Perhaps more important, the instrument does not have application restrictions.	Reference
Illumina	NovaSeq - SP	Lane	400,000,000	1x500bp, 2x250bp	SR & PE	Substitution		Reference
Illumina	NovaSeq X - 1.5B	Lane	200,000,000	2x50bp to 2x150bp	PE		High output per flow cell. Great for large whole genome, whole exome and transcriptomic projects.	Reference
Illumina	NovaSeq X - 10B	Lane	1,250,000,000	2x50bp to 2x150bp	PE		High output per flow cell. Great for large whole genome, whole exome and transcriptomic projects.	Reference
Illumina	NovaSeq X - 25B	Lane	3,250,000,000	2x50bp to 2x150bp	PE		High output per flow cell. Great for large whole genome, whole exome and transcriptomic projects.	Reference
Illumina	NovaSeq X Plus - 1.5B	Lane	206,250,000	2x50bp to 2x150bp	PE	Substitution	High output per flow cell. Great for whole genome, whole exome and transcriptomics projects.	Reference
Illumina	NovaSeq X Plus - 10B	Lane	1,250,000,000	2x50bp to 2x150bp	PE	Substitution	High output per flow cell. Great for whole genome, whole exome and transcriptomics projects.	Reference
Illumina	NovaSeq X Plus - 25B	Lane	3,331,250,000	2x50bp to 2x150bp	PE	Substitution	High output per flow cell. Great for whole genome, whole exome and transcriptomics projects.	Reference
Illumina	iSeq 100	Lane	4,000,000	1x36bp to 2x150bp	SR & PE	Substitution		Reference
PacBio	Onso	Lane	500,000,000	1x200bp to 2x150bp	SR & PE	Substitution		Reference
PacBio	RS	SMRT Cell	22,000	1x10000bp	SR	Indel		Reference
PacBio	RS II	SMRT Cell	47,000	1x10000bp	SR	Indel		Reference
PacBio	RS II (P4)	SMRT Cell	47,000	1x10000bp	SR	Indel		Reference
PacBio	RS II (P5)	SMRT Cell	47,000	1x10000bp	SR	Indel		Reference
PacBio	RS II (P6)	SMRT Cell	47,000	1x20000bp	SR	Indel		Reference
PacBio	Revio	SMRT Cell	4,500,000	15000bp to 20000bp	SR	Indel	The PacBio Revio is an upgrade to the PacBio Sequel II, as it offers higher affordability and throughput for HiFi sequencing.	Reference
PacBio	Sequel	SMRT Cell	187,500	1x20000bp	SR	Indel	PacBio's first desktop instrument delivers ~7x more reads than its predecessor.	Reference
PacBio	Sequel II	SMRT Cell	1,500,000	1x20000bp	SR	Indel		Reference
Oxford Nanopore	Flongle with kit 10/11 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Adapter that can be attached to the MinION and GridION devices for smaller, rapid tests. Especially useful and cost-effective at $90 per flow cell for running single samples or pilots.	Reference
Oxford Nanopore	Flongle with kit 12 chemistry	Flow Cell	None	typically 6-20 Kbp	SR	Indel	Adapter that can be attached to the MinION and GridION devices for smaller, rapid tests. Especially useful and cost-effective at $90 per flow cell for running single samples or pilots.	Reference
Oxford Nanopore	Flongle with kit 14 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Adapter that can be attached to the MinION and GridION devices for smaller, rapid tests. Especially useful and cost-effective at $90 per flow cell for running single samples or pilots.	Reference
Oxford Nanopore	GridION with kit 10/11 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Very flexible, as it can run 1-5 Flongle or MinION flow cells concurrently as independent runs with an integrated data processing and analysis unit. Best for larger whole genome or transcriptome projects.	Reference
Oxford Nanopore	GridION with kit 12 chemistry	Flow Cell	None	typically 6-20 Kbp	SR	Indel	Very flexible, as it can run 1-5 Flongle or MinION flow cells concurrently as independent runs with an integrated data processing and analysis unit. Best for larger whole genome or transcriptome projects.	Reference
Oxford Nanopore	GridION with kit 14 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Very flexible, as it can run 1-5 Flongle or MinION flow cells concurrently as independent runs with an integrated data processing and analysis unit. Best for larger whole genome or transcriptome projects.	Reference
Oxford Nanopore	MinION with kit 10/11 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Portable, pocket-sized and useful for when there’s a need to run real-time sequencing in the field. The low cost makes it a viable sequencing option for almost any lab for metagenomes, targeted sequencing and smaller genomes and transcriptomes.	Reference
Oxford Nanopore	MinION with kit 12 chemistry	Flow Cell	None	typically 6-20 Kbp	SR	Indel	Portable, pocket-sized and useful for when there’s a need to run real-time sequencing in the field. The low cost makes it a viable sequencing option for almost any lab for metagenomes, targeted sequencing and smaller genomes and transcriptomes.	Reference
Oxford Nanopore	MinION with kit 14 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Portable, pocket-sized and useful for when there’s a need to run real-time sequencing in the field. The low cost makes it a viable sequencing option for almost any lab for metagenomes, targeted sequencing and smaller genomes and transcriptomes.	Reference
Oxford Nanopore	PromethION 2	Flow Cell	None	Typically 6-20 Kbp	SR	Indel	The PromethION 2 Solo is a small benchtop device designed to run up to two PromethION flow cells. Each flow cell is independently addressable, meaning that experiments can be run concurrently or individually. Good in-between instrument for testing before the PromethION 24 or 48 are needed.	Reference
Oxford Nanopore	PromethION with kit 10/11 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Largest device that can run 1-48 independent flow cells on-demand and analyze the data in real time. Can generate Tb of data and is best used for very high-through sequencing for large whole genomes and transcriptomes or population-scale sequencing.	Reference
Oxford Nanopore	PromethION with kit 12 chemistry	Flow Cell	None	typically 6-20 Kbp	SR	Indel	Largest device that can run 1-48 independent flow cells on-demand and analyze the data in real time. Can generate Tb of data and is best used for very high-through sequencing for large whole genomes and transcriptomes or population-scale sequencing.	Reference
Oxford Nanopore	PromethION with kit 14 chemistry	Flow cell	None	typically 6-20 Kbp	SR	Indel	Largest device that can run 1-48 independent flow cells on-demand and analyze the data in real time. Can generate Tb of data and is best used for very high-through sequencing for large whole genomes and transcriptomes or population-scale sequencing.	Reference
Ion Torrent	GX5 Chip	Lane	15,000,000	Up to 400bp	SR	Indel		Reference
Ion Torrent	GX7 Chip	Lane	25,000,000	Up to 200bp	SR	Indel		Reference
Ion Torrent	GeneStudio S5	Chip	80,000,000	200bp to 600bp	SR	Indel		Reference
Ion Torrent	GeneStudio S5 Plus	Chip	130,000,000	200bp to 600bp	SR	Indel		Reference
Ion Torrent	GeneStudio S5 Prime	Chip	130,000,000	200bp to 600bp	SR	Indel		Reference
Ion Torrent	PGM 314 Chip	Chip	550,000	200bp to 400bp	SR	Indel		Reference
Ion Torrent	PGM 316 Chip	Chip	3,000,000	200bp to 400bp	SR	Indel		Reference
Ion Torrent	PGM 318 Chip	Chip	5,500,000	200bp to 400bp	SR	Indel	Fast turnaround time, optimal for small genomes or targeted sequencing. Compared to MiSeq, has fewer number of reads and shorter read length.	Reference
Ion Torrent	Proton I Chip	Chip	80,000,000	Up to 200bp	SR	Indel	Ion instrument with highest throughput. Compared to MiSeq, has greater number of reads but shorter read lengths.	Reference
Ion Torrent	S5/S5 XL 520 Chip	Chip	6,000,000	200bp to 600bp	SR	Indel		Reference
Ion Torrent	S5/S5 XL 530 Chip	Chip	20,000,000	200bp to 600bp	SR	Indel		Reference
Ion Torrent	S5/S5 XL 540 Chip	Chip	80,000,000	200bp	SR	Indel		Reference
Roche454	GS FLX 1 PTP	1 PTP	700,000	450bp	SR	Indel	Long read lengths make it ideal for sequencing of small genomes.
Roche454	GS FLX 1/16 PTP	1/16 PTP	20,000	450bp	SR	Indel
Roche454	GS FLX 1/2 PTP	1/2 PTP	350,000	450bp	SR	Indel
Roche454	GS FLX 1/4 PTP	1/4 PTP	125,000	450bp	SR	Indel
Roche454	GS FLX 1/8 PTP	1/8 PTP	50,000	450bp	SR	Indel
Roche454	GS FLX+ 1 PTP	1 PTP	700,000	700bp	SR	Indel	Long read lengths make it ideal for sequencing of small genomes.
Roche454	GS FLX+ 1/16 PTP	1/16 PTP	20,000	700bp	SR	Indel
Roche454	GS FLX+ 1/2 PTP	1/2 PTP	350,000	700bp	SR	Indel
Roche454	GS FLX+ 1/4 PTP	1/4 PTP	125,000	700bp	SR	Indel
Roche454	GS FLX+ 1/8 PTP	1/8 PTP	50,000	700bp	SR	Indel
Roche454	GS Junior 1 PTP	1 PTP	70,000	400bp	SR	Indel
Element Biosciences	AVITI	Flow Cell	1,000,000,000	2x75bp to 2x300bp	PE	Substitution	The Element AVITI System dramatically reduces sequencing costs while delivering high-quality data.	Reference
Complete Genomics	DNBSEQ-E25	Lane	25,000,000	1x100bp to 2x150bp	SR & PE	Substitution	Portable and easy-to-use sequencer designed to run sequencing and get the report on the go.	Reference
Complete Genomics	DNBSEQ-G400 FAST	Lane	275,000,000	1x100bp to 2x150bp	SR & PE	Substitution		Reference
Complete Genomics	DNBSEQ-G400 FCL	Lane	450,000,000	1x50bp to 2x200bp	SR & PE	Substitution		Reference
Complete Genomics	DNBSEQ-G400 FCS	Lane	275,000,000	1x100bp to 2x300bp	SR & PE	Substitution		Reference
Complete Genomics	DNBSEQ-G50 FCL	Lane	500,000,000	2x150bp	SR & PE			Reference
Complete Genomics	DNBSEQ-G50 FCS	Lane	100,000,000	2x150bp	SR & PE			Reference
Complete Genomics	DNBSEQ-G99	Lane	80,000,000	1x100bp to 2x150bp	SR & PE	Substitution	DNBSEQ-G99 is the fastest of all the medium-to-low throughput sequencers and is especially good for targeted sequencing, panel sequencing, and WGS and WES with small sample sizes.	Reference
Complete Genomics	DNBSEQ-T10×4RS	Lane	45,000,000,000	2x100bp to 2x150bp	PE		The DNBSEQ-T10×4RS is meant to be used for ultra-high throughput studies, especially useful for population research.	Reference
Complete Genomics	DNBSEQ-T20X2	Slide	40,000,000,000,000	2x100bp to 2x150bp	PE	Substitution		Reference
Complete Genomics	DNBSEQ-T7	Lane	5,000,000,000	2x100bp to 2x150bp	PE	Substitution		Reference
Singular Genomics	G4 - F2	Lane	62,500,000	2x50bp to 2x150bp	SR & PE	Subsitution	The G4’s proprietary chemistry allows it to deliver highly accurate paired-read sequencing for a variety of applications, such as RNA-Seq, Single Cell RNA-Seq, WES, Target Enrichment, Metagenomics and WGS.	Reference
Singular Genomics	G4 - F3	Lane	112,500,000	2x25bp to 2x150bp	SR & PE	Substitution	The G4’s proprietary chemistry allows it to deliver highly accurate paired-read sequencing for a variety of applications, such as RNA-Seq, Single Cell RNA-Seq, WES, Target Enrichment, Metagenomics and WGS.	Reference
Ultima Genomics	UG 100	Wafer	8,000,000,000	225bp to 300bp+	SR	Indel	New sequencer built for cost-effectiveness and accuracy with the $100 genome and $1/Gb sequencing.	Reference

*Reads/unit is the maximum value of the manufacturer's published range.

Illumina

Illumina instruments are versatile and ideal for a variety of sequencing applications, including assembly, resequencing, transcriptome, SNP detection and metagenomic studies. The HiSeq, Nextseq and GAIIx instruments are well suited for analyzing large animal or plant genomes. High level multiplexing of samples is possible when analyzing species with a smaller genome size. The HiSeq X instrument, released by Illumina in early 2014, has been been specifically designed for sequencing of whole genomes. The Illumina MiSeq outputs significantly fewer reads (Table 1), but its read lengths are significantly longer, making it ideal for small genomes, sequencing long variable domains or targeted regions within a genome. In fact, out of all the Illumina instruments, the MiSeq is best suited for amplicon-seq, 16S and other low diversity read based applications. The MiSeq Control Software (MCS) now allows users to use as little as 5% PhiX DNA spike-in to successfully sequence low-diversity samples. Other instruments, including the HiSeq and GAIIx still require at least 20-50% PhiX and are less suited for low diversity samples. The NextSeq 500, released in March of 2014, uses a two channel SBS sequencing process, likely making it even less suited for low diversity amplicons. As of 4/2014, Illumina has not performed significant validation or testing using low diversity samples on the NextSeq 500. It is not expected that the NextSeq 500 instrument will perform better than the HiSeq for these sample types. The only other major limitation of Illumina instruments compared to others in this list is their relatively short reads (2x300 is currently the longest MiSeq paired end read length).

Oxford Nanopore

Oxford Nanopore instruments are ideal for sequencing short to ultra-long fragments of native DNA or RNA and can be used for various applications. The main limitation of Oxford Nanopore sequencing is the comparatively lower read accuracy compared to short read sequencing. The relatively higher insertion and election error rates make Nanopore sequencing less optimal for single nucleotide variation/polymorphism (SNV or SNP) detection, unless you can obtain high coverage. Oxford Nanopore has improved on this limitation with the latest R10.3 chemistry, which allows for higher throughput and capture and improved raw accuracy to support enhanced variant calling.

Starting from the smallest instrument, the Flongle is an adapter for the MinION or GridION platforms and is best for amplicon sequencing, small panel/targeted sequencing, quality testing for a pilot run before a larger sequencing experiment, and running single samples on demand rather than multiplexing. The MinION is a larger, portable instrument and is best used for whole genomes, whole exomes, metagenomes, whole transcriptomes (cDNA), smaller transcriptomes (direct RNA), targeted sequencing and multiplexing for smaller samples. The GridION is a benchtop instrument designed to run up to five MinION or Flongle Flow Cells, each of which can be independently controlled in real time. The GridION is ideal for larger genomes, whole transcriptomes (direct RNA or cDNA) and a higher number of samples. The PromethION is the largest instrument and is used for high-coverage sequencing. At this level, each flow cell delivers the lowest price per Gb for nanopore sequencing, making it ideal for larger genomes, population-scale experiments, highly multiplexed small genomes or targeted regions and whole transcriptomes (direct RNA or cDNA).

Ion Torrent

The Ion PGM (Ion Torrent), is ideal for amplicons, small genomes or targeting of small regions within a genome. Its low throughput makes it ideal for smaller sized studies. The Ion Proton however is capable of generating significantly larger outputs (Table 1) making sequencing of transcriptome, exome and medium sized genomes possible.

Pacific Biosystems

The PacBio RS/RS II breaks the mold of other short reads high throughput sequencing instruments by focusing on length. The reads, averaging ~4.6 kb are significantly longer than other sequencing platforms making it ideal for sequencing small genomes such as bacteria or viruses. Other advantages include its ability to sequence regions of high G/C content and determine the status of modified bases (methylation, hydroxymethylation), eliminating the need for chemical conversion during library preparation. The instrument’s low output of reads prevent it from being useful for assembly of medium to large genomes.

Roche 454

The Roche 454 FLX+ is typically used in studies where read length is critical. These include de novo assemblies of microbial genomes, BACs and plastids. Its long read length has made it a favorite of those examining 16S variable regions and other targeted amplicon sequences. The lower output of the FLX and FLX+ instruments makes it less cost-effective for transcriptome or larger genome studies. Roche has announced that it will stop manufacturing the 454 in 2015 and end servicing in mid-2016.