2016 NGS Field Guide: Overview

These pages update the tables presented in Travis Glenn’s (2011) “Field Guide to Next Generation DNA Sequencers” for 2016 values. Previous years’ tables have been archived: 2011, 20122013, and 2014. For Travis’s overall assessment of the state of NGS technologies in 2016, see his introduction to the 2016 update.

Please note that the contents of this guide are the opinion of Travis Glenn, and do not necessarily represent those of any other organisation or person with which he is associated. Neither the other authors of this blog nor John Wiley and Sons are responsible for the accuracy of any of the information supplied by Travis.

  • Table 1a-c. “Grades” for common applications on various NGS instruments. Other information from the original table 1 is relatively static. (2014 tables)
  • Table 2. Run time, Millions of reads/run, Bases/read, and Yield/run for all common commercial NGS platforms (formerly 2a); and reagent costs/run, reagent costs/Mb, and minimum commercially available units for all common commercial NGS platforms (formerly 2b). Now presented as a sortable spreadsheet.
  • Table 3a. List purchase price for for all common commercial NGS platforms, ancillary equipment, and service contracts.
  • Table 3b. Computational resources required for all common commercial NGS platforms. (2014 table)
  • Table 3c. Errors and error rates for common commercial NGS platforms. (2014 table)
  • Table 4. Advantages and Disadvantages for all common commercial NGS platforms.

Table 0. Overall assessment of 2nd and 3rd generation DNA sequencing instruments. This table incorporates the author’s opinion for purchasing these instruments for an average U.S. university core lab, or a large molecular ecology lab, and assumes the companies will achieve stated goals consistent with past performance. This assessment combines data characteristics (amount, quality, length), cost of data and data analysis (supplies, equipment, and personnel time), as well as cost of ownership (purchase cost, downtime, and personnel costs). Major considerations are noted.

Platform – instrument Overall Ownership Assessment
Overall Score1 Notes 2016 Forecast2
Illumina – MiniSeq Yellow Light Brand New; great instrument price and features; caution due to limited users to date and limited read lengths (max ≤PE150) Stable
Illumina – MiSeq Green Light High versatility; Good fit for molecular ecologists; Owners should use NextSeq or HiSeq for large-scale projects; max ≤PE300 Slight +
Illumina – NextSeq 500/550 Green Light Reasonable balance of costs and performance for smaller facilities needing large numbers of reads (max ≤PE150) Slight +
Illumina HiSeq 1500/2500 Yellow Light Caution due to high costs & inability to use patterned flow cells; ≥3 HiSeqs needed to maximize economics; max read length ≤PE250 Stable
Illumina – HiSeq 3000/4000 Yellow Light Caution due to high costs; uses patterned flow cells; economics similar to 2500, but no Rapid Run mode; max read length ≤PE150. Stable
Illumina – HiSeq X Flashing Red Light Only available as ≥5 pack; Only authorized for ≥30x genome sequencing; ownership not currently realistic for ecologists; PE150 only Slight +
Ion Torrent – S5 Yellow Light Still relatively new; overlaps with and good choice vs. PGM & Proton; potential alternative to MiniSeq, MiSeq, & NextSeq Should Improve
Ion Torrent – PGM Flashing Red Light Caution because many PGMs are sitting idle; may be possible to find idle free or low-cost PGM; OK for very small-scale independent projects; longer reads than miniSeq. Slight +
Ion Torrent – Proton Flashing Red Light Ownership generally makes less sense than the NextSeq 500, but there are some specific situations where it can be sensible; long overdue PII is needed to make better economic sense; given S5 release, future is uncertain. Potential Zombie
Oxford Nanopore – MinION (projected) Flashing Red Light Caution due to limited output and unknowns of commercial release; Data from early access instruments has improved tremendously, but still has highest error rate of any commercial instrument. Should Improve
Oxford Nanopore – PromethION (forecast) Flashing Red Light Caution due to many unknowns; should be equal to multiple MinIONs Should Improve
Oxford Nanopore – GridION (forecast) Flashing Red Light Caution due to extensive unknowns ?
PacBio – Sequel Yellow Light Caution because it is new; Lower cost & higher throughput than RS II; Long reads & improving software; still has high error rate, but this can generally be overcome by high depth of coverage; still relatively expensive, but best current technology for multiple specific purposes, especially de novo assembly Should Improve
PacBio – RS II Red Light Specific uses make sense, but cost of ownership has never made economic sense, not clear why anyone would buy one of these now instead of a Sequel (assuming Sequel read lengths are similar) Stable, PotentialZombie
ThermoFisher – SOLiD 5500/xl/W Flashing Red Light Cost of ownership doesn’t make economic sense; limited useful applications; fading platform Potential Zombie
454 – GS Jr. Red Light Cost of ownership & use doesn’t make economic sense; Zombie platform Zombie & Death
454 – FLX+ Red Light Cost of ownership & use doesn’t make economic sense; Zombie platform Zombie & Death
Genapsys (forecast) Flashing Red Light Caution due to extensive unknowns ?
Genia (forecast) Flashing Red Light Caution due to extensive unknowns ?

Green = purchase usually sensible; Yellow = exercise caution prior to purchase, specific details of purchase, primary intended use, institutional support, logistics, and social situation will determine if this makes sense; Flashing Red = purchase may make sense in quite specific situations, come to complete stop and proceed only with extreme caution. Red = purchase generally not advised.

Forecasts are a complete guess on the author’s part and are generally based on recent announcements vs. historical trends. Should Improve = significant improvements seem likely within the next year (this is a good thing); Slight + = incremental improvements seem likely; Stable = not more than incremental improvement expected; Potential Zombie = end of platform not announced, but market seems likely to shrink; Zombie = end of platform life has been announced but hasn’t arrived (as of March 2016).

Citation

Glenn, TC. 2011. Field Guide to Next Generation DNA Sequencers. Molecular Ecology Resources. doi: 10.1111/j.1755-0998.2011.03024.x