NGS FAQ

Which are the most popular sequencing instruments and their output?

Sequencing instruments differ by chemistry, read length, throughput, run time, accuracy profile, sample flexibility and output files. This page summarises commonly encountered short-read, long-read and ultra-high-throughput systems used in research, clinical genomics and industrial sequencing projects.

Read the answer Plan a sequencing project

Quick answer

The most commonly encountered sequencing platforms include Illumina iSeq, MiniSeq, MiSeq, NextSeq, NovaSeq 6000 and NovaSeq X/X Plus; MGI DNBSEQ-G99, G400 and T7; Element AVITI and AVITI24; Thermo Fisher Ion GeneStudio S5; PacBio Sequel IIe, Revio and Vega; Oxford Nanopore MinION, GridION and PromethION; and emerging high-throughput platforms such as Ultima UG 100.

Important: output values below are approximate manufacturer specifications or commonly advertised configuration ranges. Real delivered output depends on chemistry version, flow cell, read length, library type, sample quality, loading, run time, demultiplexing, and downstream filtering.

Popular short-read sequencing instruments

Short-read systems are widely used for targeted panels, RNA-seq, exome sequencing, whole-genome sequencing, single-cell sequencing and population-scale genomics. They usually produce highly accurate reads with read lengths such as 1 × 50, 2 × 75, 2 × 150 or 2 × 300 bp depending on instrument and chemistry.

Instrument	Typical maximum output / reads	Common use cases	Notes
Illumina iSeq 100	Up to 1.2 Gb Up to 4M single reads or 8M paired-end reads per run.	Small panels, amplicons, microbial genomes, QC runs, pilot studies.	Very small benchtop SBS instrument with short turnaround.
Illumina MiniSeq	1.65–7.5 Gb 8M–25M single reads per run.	Targeted panels, small RNA-seq, small genomes, small expression projects.	Benchtop instrument positioned between iSeq and MiSeq/NextSeq.
Illumina MiSeq	540 Mb–15 Gb Up to 25M reads; maximum read length 2 × 300 bp.	Amplicons, 16S, small genomes, long paired-end reads, targeted sequencing.	Popular when longer short reads are needed.
Illumina NextSeq 550	16.25–120 Gb Up to 130M–400M single reads per run.	RNA-seq, exomes, panels, medium-throughput genomics.	Established mid-throughput platform; newer labs may use NextSeq 1000/2000 instead.
Illumina NextSeq 1000 / 2000	10–540 Gb P1 to P4 flow cells; up to 1.8B single reads or 3.6B paired-end reads with P4 on NextSeq 2000.	Bulk RNA-seq, single-cell sequencing, exomes, panels, microbial and metagenomic projects.	Flexible mid- to high-output benchtop platform with XLEAP-SBS chemistry options.
Illumina NovaSeq 6000	Up to 6 Tb/run Dual S4 runs can generate up to 20B single reads.	Human WGS, large RNA-seq projects, exomes, methylation, population studies.	Widely used production platform; increasingly complemented or replaced by NovaSeq X in some centres.
Illumina NovaSeq X / X Plus	~165 Gb–21 Tb ~1.6B–52B reads per run; maximum read length 2 × 300 bp.	Production-scale WGS, large cohorts, single-cell projects, multi-omics, deep sequencing.	Current Illumina ultra-high-throughput platform; X Plus can run dual flow cells.
MGI DNBSEQ-G99	~8–240 Gb/run Commonly configured for fast PE150 runs and low- to mid-throughput projects.	Targeted sequencing, small genomes, microbial projects, fast-turnaround NGS.	DNBSEQ chemistry; output depends on flow cell and read configuration.
MGI DNBSEQ-G400	550M–1.8B reads/run FCS: 550M reads; FCL: 1.8B reads.	WGS, RNA-seq, exomes, metagenomics, methylation, population studies.	Flexible workhorse DNBSEQ platform for day-to-day sequencing.
MGI DNBSEQ-T7	Up to 24B reads/run	Population-scale WGS, transcriptomics, metagenomics, methylation, multiomics.	High-throughput production system with multiple flow cells.
Element AVITI	Up to ~2B reads/run Cloudbreak UltraQ example: 240 Gb and 800M reads for 2 × 150.	RNA-seq, exomes, panels, single-cell, flexible benchtop sequencing.	Avidity-based chemistry; marketed for high-quality output and flexible run sizes.
Element AVITI24	Higher AVITI output Supported configurations increase sequencing output by about 50% versus standard AVITI runs.	Higher-throughput sequencing and cytoprofiling-enabled workflows.	Use current Element specifications for exact kit and output configuration.
Thermo Fisher Ion GeneStudio S5 Series	15–50 Gb/day S5: 15 Gb; S5 Plus: 30 Gb; S5 Prime: 50 Gb maximum daily throughput depending on chip.	Targeted panels, oncology panels, inherited disease panels, infectious disease sequencing.	Semiconductor sequencing; especially common in targeted clinical and translational workflows.

Popular long-read sequencing instruments

Long-read sequencing is used when read length itself is biologically valuable: genome assembly, structural variants, phasing, repeat expansions, full-length transcripts, complex regions, microbial assemblies, methylation and haplotype-resolved analysis.

Instrument	Typical maximum output / reads	Common use cases	Notes
PacBio Sequel IIe	~30 Gb/run listed by PacBio comparison Runs one SMRT Cell per run.	HiFi long-read projects, genome assemblies, structural variants, isoforms.	Established HiFi system; Revio provides much higher throughput.
PacBio Revio	120–480 Gb/run 1–4 SMRT Cells per run; up to 480 Gb HiFi reads per day.	Human long-read WGS, de novo assembly, structural variation, methylation, pangenomes.	High-throughput PacBio HiFi platform with onboard analysis.
PacBio Vega	~60 Gb/run One SMRT Cell per run.	Smaller HiFi projects, microbial genomes, targeted long-read sequencing, pilot studies.	Lower-throughput PacBio HiFi option compared with Revio.
Oxford Nanopore MinION	Up to ~50 Gb/flow cell Output depends strongly on library, run time and flow-cell condition.	Portable sequencing, rapid pathogen sequencing, amplicons, metagenomics, field genomics, long reads.	Very flexible single-flow-cell nanopore device; real-time analysis and very long reads.
Oxford Nanopore GridION	Up to 5 MinION flow cells Runs and analyses up to five MinION or Flongle flow cells simultaneously.	Multi-project nanopore sequencing, microbial genomics, metagenomics, transcriptomics, structural variants.	Benchtop scaling of MinION-style flow cells with onboard compute.
Oxford Nanopore PromethION 2 Solo / Integrated	Up to 2 PromethION flow cells PromethION flow cells produce substantially more data than MinION flow cells.	Medium-throughput long-read genomes, metagenomics, methylation, transcriptomics.	P2 Solo requires external compute; P2 Integrated includes onboard compute.
Oxford Nanopore PromethION 24	Up to 24 PromethION flow cells	High-throughput nanopore WGS, large genomes, population-scale long-read sequencing.	Production-scale nanopore platform with real-time data generation.

Ultra-high-throughput and emerging production systems

Some instruments are designed primarily for very large studies, national-scale genomics, industrial sequencing services and population-level projects.

Instrument	Typical maximum output / reads	Common use cases	Notes
Illumina NovaSeq X Plus	Up to ~21 Tb/run Up to ~52B reads per run in advertised configurations.	Population-scale WGS, large single-cell and multi-omics projects, production sequencing.	Very high throughput; sample batching and demultiplexing design are critical.
MGI DNBSEQ-T7	Up to 24B reads/run	Large WGS, RNA-seq, methylation, multiomics and metagenomic projects.	High-throughput DNBSEQ production platform.
Ultima Genomics UG 100 with Solaris	10–12B reads/wafer Up to 3.6 Tb per wafer reported for Solaris configurations.	Very large-scale short-read sequencing and cost-sensitive production genomics.	Emerging production-scale platform; evaluate application compatibility and local service availability.
Oxford Nanopore PromethION 24	24 high-output flow cells	High-throughput long-read sequencing and real-time nanopore analysis.	Actual output per flow cell varies widely with library quality and read length distribution.
PacBio Revio	Up to 480 Gb HiFi/day	High-quality long-read genomes, structural variants, assemblies, methylation and pangenomes.	Best considered by HiFi yield, read length distribution and genome coverage, not only Gb output.

What “output” means in practice

Manufacturer output is only the beginning. For project planning, it is more important to calculate usable reads or usable bases after demultiplexing, quality filtering, mapping, duplicate handling and target-region filtering.

Gb per runTotal bases generated. Useful for WGS and large projects, but does not capture read count, mapping rate or quality.

Reads per runNumber of reads or read pairs. Important for RNA-seq, single-cell sequencing, amplicons and library-complexity planning.

Usable outputReads that pass filtering and remain informative for the biological question. Often lower than raw output.

Molecular outputFor UMI assays, the number of original molecules may matter more than raw reads or raw Gb.

The same 100 Gb can mean very different things depending on whether it is 2 × 150 bp RNA-seq, long-read WGS, targeted panel sequencing, single-cell data or amplicon sequencing.

How to choose a sequencing platform

Project need	Usually suitable instruments	Decision points
Small targeted panels	iSeq, MiniSeq, MiSeq, Ion GeneStudio S5, DNBSEQ-G99, AVITI low-output configurations.	Required depth, read length, panel chemistry, turnaround, local availability.
16S / amplicons	MiSeq, iSeq, MiniSeq, DNBSEQ-G99, MinION, AVITI.	Read length, paired-end overlap, error correction, taxonomic resolution.
Bulk RNA-seq	NextSeq, NovaSeq, DNBSEQ-G400/T7, AVITI, NovaSeq X.	Reads per sample, replicate number, strandedness, batch design.
Human WES	NextSeq 1000/2000, NextSeq 550, NovaSeq, DNBSEQ-G400, AVITI.	Target coverage, uniformity, number of samples, capture chemistry.
Human short-read WGS	NovaSeq 6000, NovaSeq X/X Plus, DNBSEQ-T7, Ultima UG 100, DNBSEQ-G400 for smaller batches.	Coverage, cost per genome, batching, downstream compute and storage.
Human long-read WGS	PacBio Revio, PacBio Sequel IIe, Oxford Nanopore PromethION, GridION for smaller batches.	HiFi vs nanopore, structural variants, methylation, read length, assembly goals.
Single-cell RNA-seq	NextSeq 2000, NovaSeq, NovaSeq X, DNBSEQ-G400/T7, AVITI, Ultima UG 100 for very large batches.	Read pairs per cell, cell number, index design, lane balance, saturation.
Rapid pathogen sequencing	MinION, GridION, MiSeq, iSeq, MiniSeq, DNBSEQ-G99.	Turnaround time, portability, reference databases, sample prep speed.

Recommended platform-selection workflow

1. Define endpointVariant calling, expression, assembly, methylation, metagenomics, single-cell or custom output.

2. Choose read typeShort reads, long reads, HiFi reads, nanopore reads or hybrid strategy.

3. Estimate depthCalculate reads, Gb, flow cells, lanes, cells or molecules needed per sample.

4. Plan filesEstimate FASTQ, BAM/CRAM, POD5, VCF, count matrices, tracks and storage needs.

5. Check logisticsSample type, input amount, shipping, run batching, turnaround and provider availability.

6. Match analysisAligners, callers, demultiplexing, basecalling, QC and annotation must match platform.

7. Validate outputUse run QC, mapping metrics, coverage, duplication and saturation to assess success.

8. DocumentReport instrument, chemistry, run mode, read length, output, software and limitations.

Common mistakes

Comparing instruments by Gb onlyRead length, read count, quality, error mode, application and usable mapped data matter as much as total Gb.

Ignoring storage and computeHigh-output runs can produce large FASTQ, BAM/CRAM, POD5 and intermediate files that require proper transfer and storage planning.

Using short reads when long reads are neededRepeat expansions, phasing, structural variants and genome assembly often benefit from long reads.

Using long reads when high-count short reads are betterMany RNA-seq, panel, single-cell and standard variant projects are still efficiently handled by short-read platforms.

Ignoring demultiplexing balanceUneven sample pooling can make nominal run output misleading for individual samples.

Forgetting platform-specific error profilesBioinformatics tools and QC thresholds must reflect whether errors are mostly substitutions, indels, homopolymer-related or read-length-dependent.

How SciBerg can support instrument and output planning

SciBerg can help research and industrial partners choose a sequencing strategy, plan data output and prepare a reproducible bioinformatics workflow.

Comparison of sequencing instruments for specific project goals.
Read-depth, genome-coverage and sample-multiplexing calculations.
Short-read, long-read or hybrid sequencing strategy design.
Expected file-size and data-transfer planning.
FASTQ, BAM/CRAM, VCF, count matrix, POD5 and report deliverable planning.
Platform-specific QC, alignment, variant calling, transcriptomics and metagenomics workflows.
AI-assisted project planning, report drafting and literature-guided interpretation.

Frequently asked questions

Which sequencing instrument is best for small targeted projects?

For small targeted projects, common choices include Illumina iSeq 100, MiniSeq, MiSeq, Thermo Fisher Ion GeneStudio S5, MGI DNBSEQ-G99, Oxford Nanopore MinION, or small AVITI configurations. The best option depends on read length, turnaround time, expected depth, panel design, and whether short or long reads are required.

Which sequencing instruments are commonly used for high-throughput human WGS?

Large-scale human whole-genome sequencing is commonly performed on high-throughput short-read platforms such as Illumina NovaSeq X/X Plus, NovaSeq 6000, MGI DNBSEQ-T7 and, in some production settings, Ultima UG 100. PacBio Revio is widely used when high-accuracy long-read HiFi genomes are required.

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

Gigabases describe the total number of bases generated, while read count describes the number of sequencing reads or read pairs. A run with longer reads can generate more Gb even with the same number of reads.

Are manufacturer output values guaranteed?

No. Manufacturer values are usually specifications, nominal outputs, or maximum outputs under defined conditions. Real output depends on library quality, loading, insert size, read length, chemistry, flow-cell performance, instrument maintenance and run configuration.

Which instruments produce long reads?

Oxford Nanopore MinION, GridION and PromethION instruments produce nanopore long reads, including ultra-long reads when library quality supports them. PacBio Sequel IIe, Revio and Vega produce highly accurate HiFi long reads.

Can SciBerg help compare sequencing platforms for a project?

Yes. SciBerg can help compare sequencing instruments, read length, expected output, sample multiplexing, depth requirements, file sizes, and bioinformatics consequences for research and industrial bioinformatics projects.

Selected official sources and product specifications

These links point to official provider pages and documentation where possible. Always confirm current output values, read lengths, chemistry versions and regional availability directly with the provider or sequencing core.

Illumina iSeq 100 specifications Illumina MiniSeq specifications Illumina MiSeq specifications Illumina NextSeq 1000/2000 specifications Illumina NovaSeq 6000 specifications Illumina NovaSeq X specifications MGI DNBSEQ-G99 specifications MGI DNBSEQ-G400 specifications MGI DNBSEQ-T7 specifications Element AVITI specifications Thermo Fisher Ion GeneStudio S5 models PacBio Sequel, Vega and Revio comparison PacBio Revio system Oxford Nanopore MinION specifications Oxford Nanopore GridION specifications Oxford Nanopore PromethION 2 Solo specifications Oxford Nanopore PromethION 24 Ultima Genomics UG 100 platform