BioMed Research International / 2012 / Article / Tab 1

Review Article

Comparison of Next-Generation Sequencing Systems

Table 1

(a) Advantage and mechanism of sequencers. (b) Components and cost of sequencers. (c) Application of sequencers.

Sequencer454 GS FLXHiSeq 2000SOLiDv4Sanger 3730xl

Sequencing mechanismPyrosequencingSequencing by synthesisLigation and two-base codingDideoxy chain termination
Read length700 bp50SE, 50PE, 101PE50 + 35 bp or
50 + 50 bp
4 0 0 ∼ 9 0 0  bp
Accuracy99.9%*98%, (100PE)99.94% *raw data99.999%
Reads1 M3 G1200~1400 M
Output data/run0.7 Gb600 Gb120 Gb1.9~84 Kb
Time/run24 Hours3~10 Days7 Days for SE
14 Days for PE
20 Mins~3 Hours
AdvantageRead length, fastHigh throughputAccuracyHigh quality, long read length
DisadvantageError rate with polybase more than 6, high cost, low throughputShort read assemblyShort read assemblyHigh cost low throughput


Sequencers454 GS FLXHiSeq 2000SOLiDv43730xl

Instrument priceInstrument $500,000, $7000 per runInstrument $690,000, $6000/(30x) human genomeInstrument $495,000, $15,000/100 GbInstrument $95,000, about $4 per 800 bp reaction
CPU2* Intel Xeon X56752* Intel Xeon X55608* processor 2.0 GHzPentium IV 3.0 GHz
Memory48 GB48 GB16 GB1 GB
Hard disk1.1 TB3 TB10 TB280 GB
Automation in library preparationYesYesYesNo
Other required deviceREM e systemcBot systemEZ beads systemNo
Cost/million bases$10$0.07$0.13$2400


Sequencers454 GS FLXHiSeq 2000SOLiDv43730xl

De novoYesYesYes
High GC sampleYesYesYes
Large genomeYesYes
Mutation detectionYesYesYesYes

(1) All the data is taken from daily average performance runs in BGI. The average daily sequence data output is about 8 Tb in BGI when about 80% sequencers (mainly HiSeq 2000) are running.
(2) The reagent cost of 454 GS FLX Titanium is calculated based on the sequencing of 400 bp; the reagent cost of HiSeq 2000 is calculated based on the sequencing of 200 bp; the reagent cost of SOLiDv4 is calculated based on the sequencing of 85 bp.
(3) HiSeq 2000 is more flexible in sequencing types like 50SE, 50PE, or 101PE.
(4) SOLiD has high accuracy especially when coverage is more than 30x, so it is widely used in detecting variations in resequencing, targeted resequencing, and transcriptome sequencing. Lanes can be independently run to reduce cost.