Next-generation sequencing technologies and applications for human genetic history and forensics

Investigative Genetics

Table 1 Characteristics of second-generation and third-generation sequencing instruments

Instrument	Read length (nucleotides)	No. of reads^a	Output (Gb)^a	No. of samples^{a, b}	Runtime	Advantages	Disadvantages
Roche 454 GS FLX+	700^c	1 × 10⁶	0.7	192^d	23 h	Long reads, short run time	Homopolymer errors, expensive
Illumina HiSeq2000	100^e	3 × 10⁹	600	384	11 days^f	High yield	No. of index tags limiting
Life Technologies SOLiD 5500xl	75^g	1.5 × 10⁹	180	1,152	14 days^f	Inherent error correction	Short reads^g
Roche 454 GS Junior	400^c	1 × 10⁵	0.035	132	9 h	Long reads	Homopolymer errors, expensive
Illumina MiSeq	150	5 × 10⁶	1.5	96	27 h	Short run time, ease of use	Expensive per base
Ion Torrent PGM Ion 316 chip	> 100^h	1 × 10⁶	0.1	16	2 h	Short run time, low reagent cost	Not well evaluated
Helicos BioSciences HeliScope	35^h	1 × 10⁹	35	4,800	8 days	SMS, sequences RNA	Short reads, high error rate
Pacific Biosciences PacBio RS	> 1,000^h	1 × 10⁵	0.1	1	90 min	SMS, long reads, short run time	High error rate, low yield

Most of this information is subject to rapid change, and the aim of this table is not to present absolute numbers but to provide a general comparison between different sequencing systems.
^aNumbers calculated for two flow cells on HiSeq2000 and SOLiD 5500xl.
^bCalculated as no. of index tags (provided by the sequencing company) × no. of divisions on solid support.
^cAverage for single-end sequencing, paired-end reads are shorter.
^dNo. of reads decreases when the PicoTiterPlate is divided.
^e36 nucleotides for mate-pair reads.
^fRun time depends on the read length, and on whether one or two flow cells are used.
^gSecond read in paired-end sequencing is limited to 35 nucleotides, and mate pair reads to 60 nucleotides.
^hAverage.
SMS = single molecule sequencing.

ISSN: 2041-2223