2011 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.

N.B. If you think that these data are inaccurate or out of date, please post a comment below and we’ll attempt to include it in our next update (currently scheduled for May 2012).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 Computational Resources a Data File Sizes (GB) b
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 20 pulsed, 2 Fastq
Ion Torrent – 314 chip desktop – $35 0.1 Fastq
Ion Torrent – 316 chip    desktop – $35 0.6 Fastq
Ion Torrent – 318 chip    desktop – $35 TBD
SOLiD – 4 $35 clusterc 680d
SOLiD – 5500 $35 clusterc 74e*
SOLiD – 5500xl $35 clusterc 148e*
Illumina MiSeq desktop 1e*
Illumina HiScanSQ $222 clusterf 50e*
Illumina GAIIx $222 clusterf 600
Illumina HiSeq 1000    $222 clusterf ≤300e*
Illumina HiSeq 2000 $222 clusterf ≤600e*

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 transferred from instrument server to offline cluster

c Compute cluster available from Life Technologies

d 85Gb run is a 2×50 run (the highest throughput on a SOLiD 4)

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).

~ = Indicates a likely value based on unpublished information available in May 2011 (i.e., author speculation)

  • Information based on company sources alone (independent data not yet available); also applies to Illumina TruSeq v3 chemistry