2016 NGS Field Guide – Table 4 – Advantages & Disadvantages

Table 4. Primary advantages and disadvantages of each next-generation sequencing instrument.

Instrument Primary Advantages Primary Disadvantages
3730xl (capillary) Low cost for very small studies Very high cost for large amounts of data
Illumina MiniSeq Low instrument cost; should be simple to use; much lower cost data than MiSeq Nano & Micro kits Limited to PE150; High output PE150 kits are relatively expensive; newness creates unknowns
Illumina MiSeq Moderate cost instrument and runs; Low cost per Mb for a small platform; Fastest Illumina run times and longest Illumina read lengths Relatively few reads and Higher cost per Mb compared to NextSEq or HiSeq
Illumina NextSeq 500 Easy to use; Moderate instrument and run costs; Flow cells with room to grow Version 2 of new chemistry still not as good as older chemistry (used on MiSeq & HiSeq)
Illumina HiSeq 2500 Low cost per MB of data; can run high output (8 lane) and rapid run (2 lane) flow cells with several possible read-length configurations High instrument cost; high cost per run; requires highly trained personnel; ~20% downtime; can’t run one rapid run and one high output flow cell at the same time
Illumina HiSeq 4000 Patterned flow cells; low cost per read & per MB Similar to HiSeq 2500, but even more expensive; not as flexible as the HiSeq 2500
Illumina HiSeq X Five (or Ten) Current lowest cost per read or per MB Requires ≥$6M plus more data storage than imaginable; only authorized for ≥30x genome resequencing
Ion Torrent – PGM Low cost instrument upgraded through disposable chips (the chip is the machine); very simple machine with few moving parts; three chips available with varying numbers of reads More hands-on time and fewer reads at higher cost per Mb relative to MiSeq; smaller user community; libraries made for 400 base reads don’t work well on Proton
Ion Torrent – Proton Moderate cost instrument for medium throughput applications; similar cost to NextSeq, but PII to actually deliver similar reads as NextSeq is years overdue More hands on time, and fewer overall bases of data than Illumina; Higher cost per MB of data than most Illumina instruments; smaller user community
Ion Torrent – S5/S5 xl Cost-competitive vs. MiSeq, potentially NextSeq; brightest future among Ion Torrent instruments User community not yet established for molecular ecology; Fewer data analysis tools & pipelines
Oxford Nanopore minION SMALL PORTABLE Instrument; It is a USB device; extremely low-cost instrument; extremely long reads feasible (multiple kb) Weird quasi-commercial release; error-rates only now approaching what was promised in 2012; biased errors; High cost per read
Oxford Nanopore PromethION * (forecast) Should be similar to an array of MinIONs to increase throughput & decrease costs Similar to or same as MinION; Not yet available
PacBio – RS II Single molecule real-time sequencing; Longest available read length among well established platforms; Ability to detect base modifications; Short instrument run time; Random error profile; Modest cost per sample; Excellent for full genome assembly with sufficient coverage High error rates so high coverage is necessary; Low total number of reads per run; High cost per Mb; High capital cost; Many methods still in development; past company performance not very good (though markedly improved recently)
PacBio – Sequel Lower cost for instrument, data & service contract relative to RS II; otherwise should be similar to RSII New, thus limited info from non-company sources; High cost per Mb and per read relative to other platforms; should be similar to RS II
ThermoFisher SOLiD – 5500/5500xl/5500W Each lane of Flow-Chip can be run independently; High accuracy; Output in bases (not color-space); Ability to rescue failed sequencing cycles; 96 validated barcodes per lane; Throughput of 20-30Gb/day Longevity of Platform; Relatively short reads; more gaps in assemblies than Illumina data; less even data distribution than Illumina; High capital cost
454 GS Jr. Zombie Support of platform ending in mid-2016; not sure why they still have “active” information on their website
454 FLX+ Zombie Support of platform ending in mid-2016; not sure why they still have “active” information on their website

Mb = Megabase; Gb = Gigabase; * Information based on company sources alone (independent data not yet available)