2014 NGS Field Guide: Overview

These pages update the tables presented in Travis Glenn’s (2011) “Field Guide to Next Generation DNA Sequencers” for 2014 values. Previous years’ tables have been archived: 2011, 2012, and 2013.

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.
  • 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.
  • Table 3c. Errors and error rates for common commercial NGS platforms.
  • 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 of these instruments for an average U.S. university core lab or 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 Assessment

Overall Score

Notes

Accept if Free1

Illumina – MiSeq Green Light High versatility; Good fit for molecular ecologists; Owners should still use HiSeqs when economically best to do so Yes
Illumina – NextSeq 500 Green Light Good for higher throughput than MiSeq; ** Yes
Illumina HiSeq 2500 Yellow Light Caution due to high costs; it takes ~3 HiSeqs to maximize economics Probably
Illumina – HiSeq X (projected) Yellow Light Caution due to high costs; currently only available in 10-pack for human genome resequencing Probably
Ion Torrent – PGM Red/Yellow Light Caution because most of these instruments are sitting idle; finding available machine time is not difficult; consider a used one; may be possible to find one for free or at low cost, especially within large institutions Probably Not
Ion Torrent – Proton Yellow Light Ownership makes much less sense with the introduction of the NextSeq 500 and HiSeq X; May make sense in some circumstances if the Proton II and III chips deliver on promises and NextSeq 500 and/or HiSeq X don’t. Probably
PacBio – RS Red Light Cost of ownership has never made economic sense; there are plenty of machines with time available No
454 – GS Jr. Red Light Cost of ownership & use doesn’t make economic sense; Zombie platform No
454 – FLX+ Red Light Cost of ownership & use doesn’t make economic sense; Zombie platform No
Life Technologies – SOLiD 5500/xl/W Red Light Cost of ownership doesn’t make economic sense; limited useful applications; fading platform No
Oxford Nanopore – minION Yellow Light Excellent read lengths, but caution due to limited output and high error rates Yes
GridION (forecast) Yellow Light Caution due to unknowns Yes

1 If I were offered one of these instruments for free, would I take it and keep it? Probably generally indicates a desire to place the instrument into a core lab that already has ≥1 of these instruments (which may not be local & thus would require some pain to arrange). Note: I would accept any instrument if I could turn around and sell it and keep the cash.

** NextSeq caveats – only a single pool is loaded across all 4 lanes, so high indexing capability is needed for most molecular ecology applications; only 96 indexes are supported on BaseSpace, so be prepared to deal with a new 2nd index read primer location (BaseSpace automatically reverse complements the i5’s for NextSeq; bcl to fastq does not); invisible G’s may cause issues with custom indexes and a very few specific sequencing situations

Citation

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