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Next-generation sequencing technologies are being updated constantly so sometimes it is hard to choose the technology that is best for your research. Below we’ve collected an unofficial table to help compare the instruments that were current at the beginning of 2016.

*Note: We assembled this list from experience, vendor sites, other cores, and word-of-mouth. Please let us know if you find any errors.

YesYes

Illumina IonTorrent PacBio
Instrument MiSeq NextSeq HiSeq PGM S5 Proton RS II Sequel System*
Technology Strength Sequencing depth Combination Read length
Available at V. Core ?  YES
Total Workflow Time ~2-5 days ~3 days ~8 days ~3 days ~3-4 days ~2 days ~1 day
Typical Price per library prep $172 >$147 >$155 $206 $206 $172 >$309
Typical Price per run $823 – $1,750 >$1,143 $913 – $2,449 $1,339 $1,339-1,715 $1,199 $699
Read length of output (bp) 300 75-300 36 – 250 200-400 200-600 200 >20,000 >20,000
# of reads per run 25M 130-400M 300M – 4B 4 – 5.5M 15 – 80M 60 – 80M 0.055M 0.385M
Sequencing time (h) ~56 ~11-29 ~144 7 7 – 22 2 – 4 0.5 – 4 0.5 – 6
Data size of output (GB) 15 16-120 9 – 1000 1.2 – 2 6 – 15 10 0.5 – 1 3.5 – 7
Uses amplification of template ? Yes Yes Yes Yes Yes Yes No No

*introduced Sep 2015

References:

Miseq: http://www.illumina.com/systems/miseq.html , http://www.illumina.com/systems/miseq/performance_specifications.html
NextSeq: http://www.illumina.com/systems/nextseq-sequencer.html
Hiseq2000: http://www.illumina.com/Documents/systems/hiseq/datasheet_hiseq_systems.pdf

PGM: https://tools.thermofisher.com/content/sfs/brochures/PGM-Specification-Sheet.pdf
S5: https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-s5-ngs-targeted-sequencing/ion-s5-specifications.html
Proton: https://tools.thermofisher.com/content/sfs/brochures/CO06326_Proton_Spec_Sheet_FHR.pdf

RS II: http://www.pacb.com/wp-content/uploads/2015/09/PacBio_RS_II_Brochure.pdf
Sequel: http://www.pacb.com/wp-content/uploads/2015/09/Revolutionize-Genomics-with-SMRT-Sequencing.pdf

Others’ comparison of different sequencing technologies:

http://www.biomedcentral.com/1471-2164/15/96
http://www.nature.com/news/next-generation-genome-sequencers-compared-1.10497