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.

NGS Platforms

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 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 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 1x300bp, 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 2x150bp SR & PE Substitution v3 chemistry offers fewer reads per lane compared to v4 Reference
Illumina HiSeq High-Output v4 Lane 250,000,000 1x250bp, 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 1x500bp, 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, designed for human and non-human whole human genome seqencing. Reference
Illumina MiSeq Lane 5,000,000 2x250bp SR & PE Substitution Reference
Illumina MiSeq v2 Lane 17,000,000 2x250bp SR & PE Substitution Reference
Illumina MiSeq v2 Micro Lane 4,000,000 2x150bp SR & PE Substitution Reference
Illumina MiSeq v2 Nano Lane 1,000,000 2x250bp SR & PE Substitution Reference
Illumina MiSeq v3 Lane 25,000,000 2x300bp SR & 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 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 SR & 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 500 High-Output Run 400,000,000 1x300bp, 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 2x150bp PE Substitution Reference
Illumina NextSeq 500 v2 High-Output Run 400,000,000 1x300bp, 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 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 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 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 High output per flow cell. Great for whole genome, whole exome and transcriptomics projects. Reference
Illumina iSeq 100 Lane 4,000,000 2x150bp SR & PE Substitution Reference
PacBio PacBio RS SMRT Cell 22,000 4500bp SR Indel Reference
PacBio PacBio RS II SMRT Cell 47,000 4600bp SR Indel Reference
PacBio PacBio RS II (P4) SMRT Cell 47,000 5500bp SR Indel Reference
PacBio PacBio RS II (P5) SMRT Cell 47,000 8500bp SR Indel Reference
PacBio PacBio RS II (P6) SMRT Cell 47,000 20000bp SR Indel Reference
PacBio PacBio Revio SMRT Cell 4,500,000 1x20000 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 PacBio Sequel SMRT Cell 187,500 20000bp SR Indel PacBio's first desktop instrument delivers ~7x more reads than its predecessor. Reference
PacBio PacBio Sequel II SMRT Cell 1,500,000 20000bp SR Indel Reference
Oxford Nanopore Flongle with kit 10/11 chemistry Flow cell None typically 6-20 Kbp SR Indel & substitution 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 & substitution 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 & substitution 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 & substitution 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 & substitution 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 & substitution 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 & substitution 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 & subsitution 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 & substitution 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 & substitution 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 & substitution 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 & substitution 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 & substitution 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 PGM 314 Chip Chip 400,000 400bp SR Indel Reference
Ion Torrent PGM 316 Chip Chip 2,000,000 400bp SR Indel Reference
Ion Torrent PGM 318 Chip Chip 4,000,000 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 60,000,000 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 5,000,000 400bp SR Indel Reference
Ion Torrent S5/S5 XL 530 Chip Chip 20,000,000 400bp 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 2x25bp to 2x150bp PE The Element AVITI System dramatically reduces sequencing costs while delivering high-quality data. Reference
Complete Genomics DNBSEQ-E25 Lane 25,000,000 1x100 to 2x150bp SR & PE 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 2x150bp SR & PE Reference
Complete Genomics DNBSEQ-G400 FCL Lane 450,000,000 1x400bp, 2x200bp SR & PE Reference
Complete Genomics DNBSEQ-G400 FCS Lane 275,000,000 2x150bp SR & PE 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 1x35bp to 2x150bp SR & PE 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-T7 Lane 5,000,000,000 2x150bp PE Reference
Singular Genomics G4 - F2 Lane 62,500,000 2x50bp to 2x150bp PE 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 2x50bp to 2x150bp PE 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

*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.

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