Whole-genome sequencing in bacteriology: state of the art

Figures & data

Figure 1 Cost per megabase of sequencing, from 2001 to 2012.

Adapted from the NIH NHGRI Genome Sequencing Program website (http://www.genome.gov/sequencingcosts/).

Abbreviations: NIH, National Institutes of Health, NHGRI, National Human Genome Research Institute.

Table 1 An overview of current sequencing technologies

Platform	Run time	Sequence yield per run	Reported accuracy	Mean read length	Paired reads	Template DNA required	Reads per run
Illumina MiSeq	27 hours	8 Gb	>85% above Q30	2 × 250 bp	Yes	100 ng^−1 μg	15 M
Illumina HiSeq 1500
Rapid run	27–40 hours	60–90 Gb	>80% above Q30	2 × 150 bp	Yes	100 ng^−1 μg	300 M
High output	8.5 days	300 Gb	>80% above Q30	2 × 100 bp	Yes	100 ng^−1 μg	1.5 B
Illumina HiSeq 2500
Rapid run	27–40 hours	90–120 Gb	>80% above Q30	2 × 150 bp	Yes	100 ng^−1 μg	600 M
High output	11 days	600 Gb	>80% above Q30	2 × 100 bp	Yes	100 ng^−1 μg	3 B
Illumina GAIIx	14 days	95 Gb	>80% above Q30	2 × 150 bp	Yes	100 ng^−1 μg	320 M
PacBio RS II	2 hours	230 Mb	Approx 86% (Q8)	Approx 4,500 bp	No	250 ng^−1 μg	50 k
Ion Torrent
Ion 314 chip v2	2.3–3.7 hours	30–100 Mb	>90% above Q20	200–400 bp	Yes	100 ng^−1 μg	400–550 k
Ion 316 chip v2	3–4.9 hours	300 Mb–1 Gb	>90% above Q20	200–400 bp	Yes	100 ng^−1 μg	2–3 M
Ion 318 chip v2	4.4–7.3 hours	600 Mb–2 Gb	>90% above Q20	200–400 bp	Yes	100 ng^−1 μg	4–5.5 M
SOLiD 5500 W	2–7 days	80–160 Gb	90% above Q40	2 × 60 bp	Yes	10 ng^−5 μg	1.2 B
SOLiD 5500xl W	2–7 days	160–320 Gb	90% above Q40	2 × 60 bp	Yes	10 ng^−5 μg	2.4 B
454 GS FLX+	10–23 hours	450–700 Mb	Mostly >Q30	Up to 1 kb	Yes	700 ng^−1 μg	1 M
454 GS Jr	10 hours	35 Mb	Mostly >Q30	400 bp	Yes	700 ng^−1 μg	100 k

Notes: Illumina MiSeq, Illumina HiSeq 1500, Illumina HiSeq 2500, Illumina GAIIx (Illumina Inc., San Diego, CA, USA);Ion Torrent (Life Technologies Corporation, Grand Island, NY, USA); PacBio RS II (Pacific Biosciences Inc, Menlo Park, CA 94025); SOLiD 5500W, SOLiD 5500xl W (Sequencing by Oligo Ligation Detection)(Life Technologies Corporation, Grand Island, NY, USA). Q score = −10 log 10 P, where P is the probability of an incorrect base call. 454 GS FLX+ and 454 GS Jr (Roche Inc., Branford, CT, USA).

Abbreviation: DNA, deoxyribonucleic acid.

Table 2 Relative strengths and weaknesses of current sequencing technologies

Platform	Strengths	Weaknesses
Illumina	Low error rates	Higher indel rates
MiSeq	Support for paired end sequencing	Errors with GC-rich sequences
Illumina	Low error rates	Relatively short read lengths
HiSeq	Support for paired end sequencing
PacBio	Long read lengths(/br)Detects DNA methylation	SNP detection less sensitive due to higher individual read error length
The Ion Personal Genome Machine® (PGM™)	SNP detection	Bias with AT-rich regions
SOLiD	High accuracy Flexible configuration	Short read lengths
454	Read length	Higher indel rates
	Sequencing speed	Difficulty sequencing homopolymeric tracts

Notes: Illumina (Illumina Inc., San Diego, CA, USA); Ion Torrent (Life Technologies Corporation, Grand Island, NY, USA); PacBio (Pacific Biosciences Inc, Menlo Park, CA 94025); MySeq and HiSeq (Illumina Inc., San Diego, CA, USA), SOLiD (Sequencing by Oligo Ligation Detection)(Life Technologies Corporation, Grand Island, NY, USA)

Abbreviations: DNA, Deoxyribonucleic acid; AT, adenine and thymine, GC, guanine and cytosine, SNP, single nucleotide polymorphism.