2014 NGS Field Guide – Table 4 – Advantages & Disadvantages

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


Primary Advantages

Primary Disadvantages

3730xl (capillary)

Low cost for very small studies

Very high cost for large amounts of data

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 HiSeq

Illumina NextSeq 500

Easy to use; Moderate instrument and run costs; New chemistry and flow cells with lots of room to grow

New chemistry and new instrument design (likely to have kinks to work through)

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 X (projected)

Higher capacity and lower cost per MB than HiSeq 2500

Not projected to be available until ~2015

Illumina HiSeq X Ten

Current lowest cost per MB

Only ~2 more systems available in 2014; requires ≥$10M plus more data storage than imaginable; only authorized for human genome resequencing

Ion Torrent – PGM

Low cost instrument upgraded through disposable chips (the chip is the machine); very simple machine with few moving parts; clear trajectory to improved performance; three chips available with varying numbers of reads

Higher error rate than Illumina; 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

Moderately low-cost instrument for high throughput applications; similar cost to MiSeq, but PII and PIII chips will give more reads than MiSeq

Higher error rate, 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


Single molecule real-time sequencing; Longest available read length; Ability to detect base modifications; Short instrument run time; Random error profile; Modest cost per sample; Many methods being developed

High error rates; Low total number of reads per run; High cost per Mb; High capital cost; Many methods still in development; Weak company performance

454 GS Jr.

Lower cost per run than 454 FLX+

High cost per Mb; few reads; shorter reads than FLX+; similar instrument cost to MiSeq and PGM; support of platform ending in mid-2016

454 FLX+

Longest available contiguous reads on any 2nd generation instrument (i.e., non-single molecule instrument)

High capital cost; High cost per Mb; reagent issues; upgrade issues; support of platform ending in mid-2016

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

Oxford Nanopore minion * (projected)

SMALL PORTABLE Instrument; IT IS A USB DEVICE; extremely low-cost instrument; extremely long reads feasible (multiple kb)

Early access program starting, but instruments not yet available; No data publicly available; unknown error-rate (≤4%?); Limited information available on sample prep or data yield during 6 hour flow cell life-time; High cost per Mb relative to other Nanopore sequencers in development

Oxford Nanopore GridION * (forecast)

Extremely long reads are feasible; Low-cost instrument (node); Error-rate doesn’t increase along the length of the read; hairpin on one end allows reading of the complementary strand

Not yet available; No data publicly available; 4% error-rates; errors are likely to be biased (thus multiple reads will lead to higher confidence in the wrong answer)

Mb = Megabase; Gb = Gigabase

* Information based on company sources alone (independent data not yet available)