TABLE 1 | Comparison of next-generation sequencing platforms

From the following article:

Sequencing technologies — the next generation

Michael L. Metzker

Nature Reviews Genetics 11, 31-46 (January 2010)


PlatformLibrary/template preparationNGS chemistryRead length (bases)Run time (days)Gb per runMachine cost (US$)ProsConsBiological applicationsRefs
Roche/454's GS FLX TitaniumFrag, MP/emPCRPS330*0.350.45500,000Longer reads improve mapping in repetitive regions; fast run timesHigh reagent cost; high error rates in homo-polymer repeatsBacterial and insect genome de novo assemblies; medium scale (<3 Mb) exome capture; 16S in metagenomicsD. Muzny, pers. comm.
Illumina/ Solexa's GAIIFrag, MP/solid-phaseRTs75 or 1004, 9§18, 35§540,000Currently the most widely used platform in the fieldLow multiplexing capability of samplesVariant discovery by whole-genome resequencing or whole-exome capture; gene discovery in metagenomicsD. Muzny, pers. comm.
Life/APG's SOLiD 3Frag, MP/emPCRCleavable probe SBL507, 14§30, 50§595,000Two-base encoding provides inherent error correctionLong run timesVariant discovery by whole-genome resequencing or whole-exome capture; gene discovery in metagenomicsD. Muzny, pers. comm.
Polonator G.007MP only/emPCRNon-cleavable probe SBL265§12§170,000Least expensive platform; open source to adapt alternative NGS chemistriesUsers are required to maintain and quality control reagents; shortest NGS read lengthsBacterial genome resequencing for variant discoveryJ. Edwards, pers. comm.
Helicos BioSciences HeliScopeFrag, MP/single moleculeRTs32*837999,000Non-bias representation of templates for genome and seq-based applicationsHigh error rates compared with other reversible terminator chemistriesSeq-based methods91
Pacific Biosciences (target release: 2010)Frag only/single moleculeReal-time964*N/AN/AN/AHas the greatest potential for reads exceeding 1 kbHighest error rates compared with other NGS chemistriesFull-length transcriptome sequencing; complements other resequencing efforts in discovering large structural variants and haplotype blocksS. Turner, pers. comm.
*Average read-lengths.
Fragment run.
§Mate-pair run. Frag, fragment; GA, Genome Analyzer; GS, Genome Sequencer; MP, mate-pair; N/A, not available; NGS, next-generation sequencing; PS, pyrosequencing; RT, reversible terminator; SBL, sequencing by ligation; SOLiD, support oligonucleotide ligation detection.

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