2013 NGS Field Guide – Table 3b – Computation Resources

Table 3b. Computational resources needed and size of data files for commercially available DNA sequencing platforms in 2011. All costs are list price in thousands of US dollars.

Instrument Computational Resourcesc Data File Sizes (GB)d
3730xl (capillary) desktop 0.03
454 GS Jr. Titanium $5 (desktop) < 3 images, < 1 sff
454 FLX Titanium $5 (desktop) 20 images, 4 sff
454 FLX+ $5 (desktop) 40 images, 8 sff
PacBio RS $65 cluster 2 (basecalls, QV, kinetics)
Ion Torrent – 314 chip $16.5 (desktop)c 0.1 sff, 0.2 fastq
Ion Torrent – 316 chip $16.5 (desktop)c 5 sff, 1 fastq
Ion Torrent – 318 chip $16.5 (desktop)c 10 sff, 2.5 fastq
Ion Torrent – Proton I ($75) clusterd 120 sff, 30 fastq
Ion Torrent – Proton II ($75) clusterd [big]
Ion Torrent – Proton III* ($75) clusterd [big]
SOLiD – 5500xl $35 clusterc 148e*
Illumina MiSeq Desktop/cloud 1e*
Illumina HiScanSQ $222 clusterf 50e*
Illumina GAIIx $222 clusterf 600
Illumina HiSeq 1000 $222 clusterf ≤ 300e*
Illumina HiSeq 2000 $222 clusterf ≤ 600e*
Illumina HiSeq 2500 $222 clusterf [big]
Oxford Nanopore minION laptop [small]
Oxford Nanopore GridION 2000 ? [variable]
Oxford Nanopore GridION 8000 ? [variable]

a Desktops assume higher-end models with multiple processors, ≥ 8 GB RAM, ≥ 1 TB HD, etc. (up to $5k; except capillary = $2k desktop)

b Data file size (ballpark average) transferred from instrument server to offline cluster; Ion Torrent PGM chips = 500 cycles

c Compute cluster available from Life Technologies

d Compute cluster included as part of the Proton system (not a separate cost)

e New compressed binary data format saves base and quality-value data in a 1byte:1base ratio

f Illumina Compute – Tier 1 system: 3 cluster nodes with 8 cores and 48 GB RAM per node (i.e., 24 cores and 144 GB RAM) and ~24 TB usable data storage; commodity equivalent systems are available for much less, but will require technical support (see text).

[big/small] = general indication of size