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 - 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 - 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 i100 Plus - 100M
|
Lane |
100,000,000 |
1x100bp to 2x150bp |
SR & PE |
Substitution |
The MiSeq i100 Plus 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 Plus - 50M
|
Lane |
50,000,000 |
1x100bp to 2x300bp |
SR & PE |
Substitution |
The MiSeq i100 Plus 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 |
PacBio |
Vega
|
SMRT Cell |
3,000,000 |
1000bp to 20000bp |
SR |
Indel |
The PacBio Vega is the first HiFi benchtop system, bringing the same accuracy of the well-known long HiFi reads into a more compact system appropriate for smaller labs. |
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-G800
|
Lane |
450,000,000 |
1x50bp to 2x150bp |
SR & PE |
Substitution |
This sequencer offers a long read option at SE600 on top of the standard short reads (i.e. SE50 to PE150). The SE600 options is meant specifically for the sequencing of challenging genomic regions, such as tandem repeats, homopolymer stretches, and high GC content regions. |
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-T1+ FCL
|
Lane |
500,000,000 |
1x100bp to 2x150bp |
SR & PE |
Substitution |
The DNBSEQ-T1+ improves efficiency with onboard secondary data analysis, supporting multiple types of analysis. It's meant to be used for a diverse number of project types with 3 different flow cell types and multiple individually addressable lanes. |
Reference |
Complete Genomics |
DNBSEQ-T1+ FCM
|
Lane |
500,000,000 |
1x100bp to 2x150bp |
SR & PE |
Substitution |
The DNBSEQ-T1+ improves efficiency with onboard secondary data analysis, supporting multiple types of analysis. It's meant to be used for a diverse number of project types with 3 different flow cell types and multiple individually addressable lanes. |
Reference |
Complete Genomics |
DNBSEQ-T1+ FCS
|
Lane |
250,000,000 |
1x100bp to 2x300bp |
SR & PE |
Substitution |
The DNBSEQ-T1+ improves efficiency with onboard secondary data analysis, supporting multiple types of analysis. It's meant to be used for a diverse number of project types with 3 different flow cell types and multiple individually addressable lanes. |
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 |
Ultima Genomics |
UG 100 Solaris
|
Wafer |
12,000,000,000 |
225bp to 300bp+ |
SR |
Indel |
Updated UG 100 built for even more cost-effectiveness with 50% increase in output and 20% reduction in cost. |
Reference |