新型シーケンサーの生データサイズはどんな風ですか？

alt text [http://www.flickr.com/photos/59261391@N05/5475238349/][2] はしばらく前の議論に使った目安です。　現状はどうなんでしょうか？

Kato Kikuya Impact of the next generation DNA sequencers . Int J Clin Exp Med. 2009; 2(2): 193–202. Published online 2009 July 8. Comparison of sequencers (January, 2009). It should be noted that the throughput of each sequencer is improving rapidly

	ABI 3730xI	Roche GS FLX	Illumina GA	ABI SOLiD
Bases/template	∼1100	∼400	∼75	50
Templates/run	96	1,000,000	40,000,000	85,000,000
Data production/day	1 MB/day	400MB/run/7.5hr	3,000MB/run/6.5 days	4,000MB/run/6 days
Maximum samples	96	16 regions/plate	8 channels/flowcell	16chambers/2 slides
Sequence reaction	Sanger method	pyrosequencing	Reverse terminator	ligation sequencing

ddbj sra ngs

質問日 Feb 25 '11 at 14:48

okubo
131●5●9●13

edited Mar 01 '11 at 12:20

4 Answers:

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1	HiSeq約100bpくらいのリードの1レーンシングル分(1ファイル)で25~30GB、ペアエンド分(2ファイル)だとその2倍くらいです。1ラン8レーンなので400~480GBくらいでしょうか。回答日 Feb 25 '11 at 14:57 na 16●1 edited Feb 25 '11 at 15:06

仲里　SRA 目次をみると　次世代といってもいろいろあるのがよくわかります。数値は実験数です。　経時展開できるともっといいんですけどね

Illumina Genome Analyzer II	19786
454 GS FLX	5815
Illumina Genome Analyzer	5191
Illumina HiSeq 2000	2873
454 Titanium	2799
GS FLX	709
unspecified	577
Illumina Genome Analyzer IIx	344
AB SOLiD System 3.0	339
454 GS FLX Titanium	309
Solexa 1G Genome Analyzer	268
AB SOLiD 4 System	265
AB SOLiD System 2.0	198
GS 20	164
AB SOLiD System	118
454 GS 20	118
Helicos HeliScope	16
454 GS	11
none	5
UNKNOWN	5
Total	39910
(experiments)

回答日 Feb 27 '11 at 13:32

okubo
131●5●9●13

edited Feb 27 '11 at 13:44

Platform	Company	Sequencing data per run (single read)	2 Kb – calculated multiplexing for50x coverage	1 Mb – calculatedmultiplexing for 50x coverage
GS Junior	454 Sequencing	40 MB	400	approx. 1
GS FLX	454 Sequencing	540 MB	5,400	11
MiSeq	Illumina	510 MB	5,100	10
GA IIx	Illumina	48,000 MB	480,000	960
HiSeq2000	Illumina	100,000 MB	1,000,000	2,000
SOLiD4	Life Technologies	150,000 MB	1,500,000	3,000
AB3730xl	Life Technologies	0.08 MB	–	–

Table 1: Overview of the amount of data generated from currently available NGS platforms from the three largest competitors (based on manufacturer’s specifications) along with an estimate of thenumber of samples that could theoretically be analyzed during a single sequencing run. Next-generation Sequencing, Application in Molecular Diagnostics, M.Sc Stefan Kotschote et al., IMGM Laboratories 2011 - imgm.com

回答日 Feb 28 '11 at 22:10

okubo
131●5●9●13

Method	Amplification	Read length (base pairs)	Templates per run	Data production/day	Sequence reaction	Reference
ABI 3730xI	PCR	~900 to 1,100	96	1 Mb/day	Sanger method	http://www.appliedbyosystems.com
454 FLX Roche	Emulsion PCR	~400	1,000,000	400 Mb/run/7.5 to 8 hours	Pyrosequencing	http://www.rocheapplied-science.com
Illumina (Solexa) Genome Analyzer	Bridge PCR	36 to 175	40,000,000	>17 Gb/run/3 to 6 days	Reverse terminator	http://www.illumina.com
ABI SOLiD	Emulsion PCR	~50	85,000,000	10 to 15 Gb/run/6 days	Ligation sequencing	http://www.appliedbyosystems.com
Helicos Heliscope	None	30 to 35	800,000,000	21 to 28 Gb/run/8 days	Single molecule sequence by synthesis	http://www.helicosbio.com

Next-generation sequencing, breast-cancer-research.comJ Reis-Filho - Breast Cancer Research, 2009

Technologies in development
Pacific Biosciences	None	>1,000	NA	NA	Single molecule real-time DNA sequencing	http://www.pacificbiosciences.com
Intelligent Biosciences	Yesa	NA	NA	NA	Sequence by synthesis	http://www.intelligentbiosystems.com
Visigen Biotechnologies	None	NA	NA	NA	Base-specific FRET emission	http://www.visigenbio.com
ZS Genetics	None	NA	NA	NA	ZSG atomic labelling and electron microscopy	http://www.zsgenetics.com

回答日 Feb 28 '11 at 22:20

okubo
131●5●9●13

edited Mar 01 '11 at 13:30

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質問日: Feb 25 '11 at 14:48

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最終更新日: Mar 01 '11 at 13:30

新型シーケンサーの生データサイズはどんな風ですか？

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