2011 NGS Field Guide – Table 4 – Advantages & Disadvantages of each instrument

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

N.B. If you think that these data are inaccurate or out of date, please post a comment below and we’ll attempt to include it in our next update (currently scheduled for May 2012).

Instrument Primary Advantages Primary Disadvantages
3730xl (capillary) Low cost for very small studies Very high cost for large amounts of data
454 GS Jr. Titanium Long read length; low capital cost; low cost per experiment High cost per Mb
454 FLX Titanium Long read length High capital cost; High cost per Mb
454 XLR2 Double the maximum read length of Titanium High cost per Mb
Helicos Large numbers of reads directly from single molecules Length of reads; questionable longevity of company
PacBio Single molecule real-time sequencing; Longest available read length; Strobed reads; Each instrument run = minutes; Low cost per sample; Many methods being developed Error rates; Low total number of reads per run; High cost per Mb; High capital cost; Many methods still in development
Ion Torrent Low cost instrument upgraded through disposable chips (the chip is the machine); very simple machine with few moving parts; clear trajectory to improved performance New platform with a variety of unknowns, and some known issues at the time of release
Ion Torrent – 314 chip Low cost per sample for small studies; Short time needed on instrument; Suitable for microbial sequencing and targeted sequencing; Easily upgraded with new chips Highest cost per Mb of all NextGen platforms; Sample prep takes much longer than time on the instrument
Ion Torrent – 316 chip Same as above, upgraded due to higher density chip Sample prep time; Similar cost per Mb to 454
Ion Torrent – 318 chip Same as above, upgraded due to higher density chip; lower cost per read and Mb allows more applications Sample prep time; Similar cost to MiSeq
SOLiD – 4 EZ Bead simplifies emPCR; low-cost per Gb; throughput = 5-6 Gb/day Unusual informatics with 2-base colorspace encoding; relatively short reads; chip runs all at once
SOLiD – 5500 Each lane of Flow-Chip can be run independently; Highest accuracy*; Output in bases (not color-space); Ability to rescue failed sequencing cycles; 96 validated barcodes per lane; Throughput of 10-15Gb/day Not available until spring 2011; relatively short reads; more gaps in assemblies than Illumina data; less even data distribution than Illumina
SOLiD – 5500xl Same as 5500, but with double the throughput Same as SOLiD 5500; High capital cost
Illumina MiSeq Low cost instrument and runs; Lowest cost/Mb for small platforms; Fastest Illumina run times Relatively few reads and Higher cost/Mb compared to other Illumina platforms
Illumina HiScanSQ Versatile instrument for full catalog of Illumina arrays and sequencing; Scalable in future Higher cost/Mb than HiSeq for large amounts of data
Illumina GAIIx Lower Capital Cost than HiSeqs Slightly higher cost per Mb than HiSeq; Not as scalable in the future
Illumina HiSeq 1000 Lower instrument cost than HiSeq 2000; same number of reads/lane and cost/lane as HiSeq 2000; field upgradable to HiSeq 2000; Future scalability Not as flexible as HiSeq 2000 due to having only 1 flow cell
Illumina HiSeq 2000 Same as HiSeq 1000, but runs 2 flow cells simultaneously; Most reads, Gb per day and Gb per run, lowest cost per Mb of all platforms* High capital cost; High computation needs

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