NGS Platform Tutorial

Most popular sequencing instruments for modern NGS projects.

A practical guide to the sequencing instruments most commonly encountered in research, clinical genomics and industrial bioinformatics: benchtop short-read sequencers, production-scale short-read systems, semiconductor sequencers, high-accuracy long-read platforms and nanopore real-time sequencing devices.

Start tutorial Platform selection guide

1. Overview

“Most popular” sequencing instruments can mean different things: installed base, current sales, service-provider availability, assay compatibility or how often a platform appears in published studies. In practice, the instruments below are commonly encountered across sequencing cores, clinical research laboratories, biotechnology companies and industrial sequencing services.

Benchtop Smaller runs, targeted panels, microbial genomics, amplicons and pilot studies.

Mid-throughput RNA-seq, exomes, moderate WGS projects, single-cell and routine core-facility work.

Production scale Large cohorts, population genomics, high-depth WGS and industrial sequencing.

Practical rule: select the sequencing platform based on the biological endpoint and the required usable data, not only on the maximum advertised output.
            

2. Key concepts before comparing instruments

Sequencing instruments are usually compared by read type, read length, read count, total output, run time, accuracy profile and cost per sample.

Read length Short-read platforms often use 1 × 50, 2 × 75, 2 × 150 or 2 × 300 bp. Long-read platforms can read thousands to millions of bases depending on input DNA quality.

Reads per run Important for RNA-seq, single-cell, amplicons and multiplexing. More reads allow more samples or deeper analysis.

Gb or Tb output Total bases generated per run. Important for WGS, metagenomics and large cohort sequencing.

Usable data Output after demultiplexing, trimming, mapping, deduplication, target filtering and QC. This is what matters biologically.

3. Popular short-read sequencing instruments

Short-read sequencing remains the standard for many routine NGS applications because workflows are mature, accuracy is high, costs are predictable and bioinformatics pipelines are well established.

Instrument family	Typical role	Strengths	Common applications
Illumina MiSeq / MiSeq i100	Low-throughput and small benchtop sequencing.	Longer short reads, amplicons, microbial projects, targeted panels and quick in-house runs.	16S, small genomes, amplicons, small panels, library QC.
Illumina NextSeq 1000/2000	Mid-throughput benchtop sequencing.	Flexible output, RNA-seq, exomes, single-cell and moderately sized WGS projects.	RNA-seq, WES, panels, scRNA-seq, metagenomics.
Illumina NovaSeq 6000 / NovaSeq X	High-throughput and production-scale sequencing.	Large output, cohort sequencing, many samples per run and large core-facility workloads.	Human WGS, large RNA-seq, single-cell, exomes, methylation.
MGI DNBSEQ systems	Alternative high-throughput short-read ecosystem.	DNBSEQ chemistry, flexible platforms and strong production-scale options.	WGS, RNA-seq, panels, metagenomics, methylation, multi-omics.
Element AVITI	Flexible benchtop short-read sequencing.	Multiple output modes, dual-flow-cell design and strong mid-throughput positioning.	RNA-seq, exomes, panels, single-cell, small WGS projects.
Ion GeneStudio S5	Semiconductor targeted sequencing.	Fast runs, targeted panels and simplified workflows for some clinical-research style assays.	Oncology panels, inherited disease panels, microbial and targeted assays.

4. Illumina instruments: MiSeq, NextSeq and NovaSeq

Illumina sequencing-by-synthesis systems are widely used in NGS laboratories. They span from small benchtop instruments to ultra-high-throughput production systems.

Instrument	Approximate output / reads	Best fit	Notes
MiSeq	~300 Mb–15 Gb MiSeq v3 2 × 300 bp runs reach about 13.2–15 Gb.	Amplicons, 16S, small genomes, targeted panels.	Useful when longer paired-end short reads are needed.
MiSeq i100 / i100 Plus	~1.5–30 Gb Up to 10–200M paired-end reads depending on flow cell.	Fast benchtop runs, amplicons, microbial genomics, targeted sequencing, QC.	Newer benchtop family with short run times and room-temperature reagent features.
NextSeq 1000/2000	10–540 Gb P1 to P4 flow cells; up to 1.8B single reads or 3.6B paired-end reads on P4.	RNA-seq, WES, panels, single-cell, metagenomics, small-to-medium WGS.	Common mid-throughput choice for sequencing cores and research labs.
NovaSeq 6000	Up to ~6 Tb/run Dual S4 runs support very large output.	Large cohort sequencing, WGS, exomes, RNA-seq, methylation.	Established production-scale platform still encountered in many core facilities.
NovaSeq X / X Plus	~0.5–10.5 Tb per flow cell at 2 × 150 NovaSeq X Plus can run dual flow cells.	Population-scale WGS, large single-cell, high-volume multi-omics.	Current high-throughput Illumina family with XLEAP-SBS chemistry and integrated DRAGEN features.

5. MGI, Element Biosciences and Ion Torrent systems

These systems broaden the short-read sequencing landscape beyond the traditional Illumina ecosystem.

Instrument	Approximate output / reads	Best fit	Notes
MGI DNBSEQ-G99	8–240 Gb/run	Targeted sequencing, small genomes, microbial genomics, fast-turnaround projects.	Low-to-mid throughput DNBSEQ benchtop system.
MGI DNBSEQ-G400	FCS 550M / FCL 1800M reads	WGS, RNA-seq, panels, metagenomics, methylation and routine medium-large projects.	Dual-flow-cell flexibility and multiple read lengths.
MGI DNBSEQ-T7	~1–7 Tb / up to 4 flow cells	Large-scale genomics, WGS, transcriptomics, metagenomics and multi-omics.	Production-scale DNBSEQ system.
Element AVITI	75–300 GB per flow cell Common configurations include up to 1B reads per high-output 2 × 150 run; two 2 × 150 runs can generate up to 600 GB and 2B reads.	RNA-seq, panels, exomes, single-cell and flexible mid-throughput projects.	Dual-flow-cell benchtop system using avidity-based sequencing chemistry.
Ion GeneStudio S5 series	15–50 Gb/day Depending on S5, S5 Plus or S5 Prime system and chip configuration.	Targeted panels, oncology research panels, inherited disease panels, microbial studies.	Semiconductor sequencing with fast targeted workflows.

6. Popular long-read sequencing instruments

Long-read sequencing is selected when read length and molecule-level information are more important than simply generating many short reads.

Instrument family	Technology	Strengths	Common applications
PacBio Sequel IIe / Revio / Vega	Single-molecule real-time sequencing with HiFi read generation.	High-accuracy long reads, phasing, structural variation, de novo assembly and methylation information.	Human long-read WGS, complex regions, isoforms, microbial genomes, pangenomes.
Oxford Nanopore MinION / GridION / PromethION	Nanopore sequencing with real-time signal-based DNA/RNA analysis.	Very long reads, real-time data generation, direct RNA/DNA options, portable to production-scale instruments.	Rapid pathogen sequencing, assemblies, structural variants, methylation, metagenomics, transcriptomics.

              Long-read projects often require different library QC, DNA extraction, storage planning, alignment tools and variant callers compared with short-read workflows.
            

7. Oxford Nanopore and PacBio examples

Instrument	Typical role	Key feature	Bioinformatics note
Oxford Nanopore MinION	Portable, low-footprint long-read sequencing.	Real-time sequencing from a single small device.	Requires basecalling and careful read-length/QC interpretation.
Oxford Nanopore GridION	Benchtop multi-flow-cell nanopore sequencing.	Scales MinION-style flow cells with onboard compute.	Useful for multiple samples or higher daily throughput.
Oxford Nanopore PromethION 2 / 24	Medium to production-scale nanopore sequencing.	PromethION 24 can run up to 24 high-output flow cells.	Large long-read datasets require substantial storage and compute planning.
PacBio Revio	High-throughput HiFi long-read sequencing.	Outputs ready-to-use HiFi reads in BAM format and performs fundamental processing on instrument.	Useful for accurate long-read WGS, methylation and structural-variant studies.

8. Practical comparison: low, mid, high and production scale

Scale	Example instruments	Typical project types	Planning focus
Low throughput	MiSeq, MiSeq i100, Ion GeneStudio S5, DNBSEQ-G99, MinION.	Amplicons, small panels, microbial genomes, library QC, pilot studies.	Turnaround, read length, per-sample depth, low sample number.
Mid throughput	NextSeq 1000/2000, Element AVITI, DNBSEQ-G400, GridION.	RNA-seq, WES, moderate panels, small WGS, single-cell pilot studies.	Batching, multiplexing, run size and data analysis throughput.
High throughput	NovaSeq 6000, NovaSeq X, DNBSEQ-T7, PacBio Revio, PromethION.	Human WGS, large RNA-seq, large single-cell, cohort sequencing, long-read WGS.	Storage, compute, data transfer, QC automation and reproducible pipelines.
Production scale	NovaSeq X Plus, DNBSEQ T-series, PromethION 24, Ultima UG 100-style deployments.	Population genomics, industrial sequencing, national-scale projects.	Cost per genome, operations, automation, LIMS, regulatory and reporting infrastructure.

9. Which instrument type fits which application?

Application	Common platform type	Why
16S / amplicon sequencing	MiSeq, MiSeq i100, DNBSEQ-G99, Ion S5, MinION.	Moderate output, often longer reads, many small libraries.
Bulk RNA-seq	NextSeq, NovaSeq, AVITI, DNBSEQ-G400/T7.	Read count per sample is central; multiplexing is common.
Whole-exome sequencing	NextSeq, NovaSeq, AVITI, DNBSEQ-G400/T7.	Requires sufficient target coverage and many reads per sample.
Human short-read WGS	NovaSeq 6000, NovaSeq X, DNBSEQ-T7/T-series, Ultima-style production platforms.	Large data volume and cost per genome dominate.
Human long-read WGS	PacBio Revio, Oxford Nanopore PromethION.	Useful for structural variants, phasing, repeats and methylation.
Single-cell RNA-seq	NextSeq, NovaSeq, AVITI, DNBSEQ-G400/T7.	Large read counts and precise indexing are critical.
Pathogen surveillance	MiSeq/i100, NextSeq, DNBSEQ-G99, MinION/GridION.	Fast turnaround, flexible batching and suitable read length matter.

10. Sequencing platform selection workflow

1. Define endpoint Variants, expression, isoforms, structural variants, methylation, microbiome or assembly.

2. Choose read type Short reads, long reads, HiFi reads, nanopore reads or hybrid sequencing.

3. Estimate depth Calculate required reads, bases, coverage, cells or unique molecules.

4. Match output Choose a flow cell or instrument class that fits the project without excessive batching delay.

5. Plan analysis Select aligners, quantifiers, variant callers, QC tools and reporting requirements.

6. Review logistics Check sample input, library prep, turnaround, provider availability and data-transfer method.

11. How the instrument choice affects bioinformatics

Platform choice changes the files, QC metrics, compute requirements and interpretation strategy.

File formats Short-read projects usually start with FASTQ files. PacBio Revio can output HiFi reads in BAM. Nanopore workflows may involve POD5/FAST5, FASTQ, BAM and methylation tags.

QC metrics Illumina-style projects emphasize Q30, cluster density, duplication, insert size and mapping. Long-read projects emphasize read N50, yield, accuracy, length distribution and molecule quality.

Aligners and callers Short-read DNA-seq often uses BWA-style aligners. Long-read workflows commonly use minimap2 and specialized structural variant or assembly tools.

Storage and compute Production-scale sequencers can create terabytes per run. Storage, compression, transfer and workflow automation must be planned before sequencing.

12. Common mistakes when choosing a sequencer

Choosing by maximum Gb only Read count, read length, accuracy, error profile, turnaround and usable mapped data may matter more.

Ignoring library requirements Long-read sequencing often needs high molecular weight DNA; some degraded samples are better suited to short reads.

Underestimating storage FASTQ, BAM/CRAM, VCF, signal tracks, POD5 and intermediate workflow files can exceed the nominal run output.

Mixing platforms without planning Combining platforms can be powerful, but requires consistent references, QC thresholds and analysis assumptions.

Ignoring index design Multiplexing, index balance and index hopping can affect sample assignment and downstream interpretation.

Forgetting downstream interpretation Sequencing should be planned together with analysis, reporting and validation strategy.

13. Current trends in sequencing instruments

Sequencing platforms continue to evolve toward higher output, faster turnaround, lower sample input, improved on-instrument analysis, real-time basecalling, better long-read accuracy and more integrated informatics.

High-throughput short-read systems increasingly integrate secondary analysis and compression.
Benchtop systems are becoming faster and more accessible for smaller laboratories.
Long-read sequencing is moving from specialized use to mainstream structural-variant, assembly and methylation applications.
Nanopore platforms continue to emphasize real-time sequencing, direct molecule detection and flexible scale.
Bioinformatics automation, LIMS integration and AI-assisted interpretation are becoming part of platform selection.

14. Instrument selection cheat sheet

Project requirement	Usually consider	Reason
Small amplicon or pathogen panel	MiSeq, MiSeq i100, Ion S5, DNBSEQ-G99, MinION.	Low-to-moderate output and fast turnaround.
Routine RNA-seq	NextSeq, AVITI, DNBSEQ-G400, NovaSeq for larger batches.	Read-count scalability and mature workflows.
High-depth human WGS	NovaSeq X, NovaSeq 6000, DNBSEQ-T7/T-series.	Large output and cost efficiency per genome.
Structural variants and phasing	PacBio Revio, Oxford Nanopore PromethION.	Long reads span difficult regions and haplotypes.
Rapid field or outbreak sequencing	Oxford Nanopore MinION/GridION, small benchtop systems.	Speed, portability and real-time analysis.
Industrial or population-scale sequencing	NovaSeq X Plus, DNBSEQ production systems, Ultima-style platforms.	Throughput, automation, cost per sample and operations matter most.

Official references and specifications

Specifications can change with chemistry, flow cells and software versions. Always confirm current values with the instrument provider or sequencing service.

Illumina MiSeq i100 specifications ↗ Illumina MiSeq specifications ↗ Illumina NextSeq 1000/2000 specifications ↗ Illumina NovaSeq X specifications ↗ MGI DNBSEQ-G99 ↗ MGI DNBSEQ-G400 ↗ Element AVITI specifications ↗ Thermo Fisher Ion GeneStudio S5 models ↗ PacBio Revio ↗ Oxford Nanopore PromethION 24 ↗ Oxford Nanopore MinION ↗ Ultima Genomics UG 100 ↗

Frequently asked questions

Which sequencing instrument is the most popular?

There is no single universal answer. Popularity depends on application, region, budget, service-provider availability and required output. Illumina systems remain widely encountered for short-read sequencing, while PacBio and Oxford Nanopore are prominent long-read platforms. MGI, Element Biosciences, Thermo Fisher Ion Torrent and Ultima Genomics are also important in specific markets and applications.

Which instrument should I use for a small targeted sequencing project?

Small targeted projects often fit benchtop instruments such as MiSeq, MiSeq i100, Ion GeneStudio S5, DNBSEQ-G99, AVITI low/medium output configurations or small nanopore workflows. The choice depends on read length, depth, panel design, turnaround time and whether short or long reads are required.

Which instruments are commonly used for human whole-genome sequencing?

High-throughput human short-read WGS is commonly run on systems such as Illumina NovaSeq 6000, NovaSeq X/X Plus and MGI DNBSEQ-T7/T-series systems. Long-read human WGS is commonly associated with PacBio Revio and Oxford Nanopore PromethION systems.

What is the difference between output in Gb and number of reads?

Gigabases measure the total number of bases generated. Read count measures how many reads or read pairs were produced. A run with longer reads can produce more Gb with the same read count, while some applications care more about read count than total bases.

Are manufacturer output specifications guaranteed?

No. Specifications are usually measured under defined conditions and often with control libraries. Actual output depends on library quality, loading, insert size, sample type, reagent version, run configuration and instrument maintenance.

Can SciBerg help select a sequencing platform?

Yes. SciBerg can help research and industrial partners compare instruments, estimate read depth, plan multiplexing, define bioinformatics deliverables and evaluate whether short-read, long-read or hybrid sequencing is appropriate.