Field guide to next-generation DNA sequencers.

[ECO]

Looks like an interesting read that Newsbot missed. Link here: http://www.ncbi.nlm.nih.gov/pubmed/21592312

Field guide to next-generation DNA sequencers.
Glenn TC.
Source
Department of Environmental Health Science and Georgia Genomics Facility, Environmental Health Science Building, University of Georgia, Athens, GA 30602, USA.
Abstract
The diversity of available 2(nd) and 3(rd) generation DNA sequencing platforms is increasing rapidly. Costs for these systems range from <$100 000 to more than $1 000 000, with instrument run times ranging from minutes to weeks. Extensive trade-offs exist among these platforms. I summarize the major characteristics of each commercially available platform to enable direct comparisons. In terms of cost per megabase (Mb) of sequence, the Illumina and SOLiD platforms are clearly superior (≤$0.10/Mb vs. >$10/Mb for 454 and some Ion Torrent chips). In terms of cost per nonmultiplexed sample and instrument run time, the Pacific Biosciences and Ion Torrent platforms excel, with the 454 GS Junior and Illumina MiSeq also notable in this regard. All platforms allow multiplexing of samples, but details of library preparation, experimental design and data analysis can constrain the options. The wide range of characteristics among available platforms provides opportunities both to conduct groundbreaking studies and to waste money on scales that were previously infeasible. Thus, careful thought about the desired characteristics of these systems is warranted before purchasing or using any of them. Updated information from this guide will be maintained at: http://dna.uga.edu/ and http://tomato.biol.trinity.edu/blog/.

© 2011 Blackwell Publishing Ltd.

PMID: 21592312 [PubMed - as supplied by publisher]

[husamia]

thanks but I can't get a copy of the transcript

update:
found it here

http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.03024.x/pdf

[BadDNA]

E-mail the author ([email protected]) and he will send you a pdf. Updated tables are available at:

http://www.molecularecologist.com/next-gen-fieldguide/

[KerryOdair]

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequence reads and SNP detection performance using three commercially available next-generation sequencers, i.e., Roche Genome Sequencer FLX System (FLX), Illumina Genome Analyzer (GA), and Applied Biosystems SOLiD system (SOLiD).

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019534

[BadDNA]

That study looks good (very detailed). It is exactly what is needed to compare across platforms; someone independently running the same templates on multiple platforms (as is called for within the Field Guide). Unfortunately, the supplementary files are messed up (the first file is doc & should be excel, and the second is excel, but should be doc), so I couldn't tell when the data were collected (i.e., what version of the chemistry for each platform was used?). From the read-lengths, it looks like the data are perhaps 3 years old. I'm not tossing any stones (I have much older unpublished data), but the chemistry & performance is a moving target. The 454 data are probably still pretty relevant (and surprisingly good), but I would guess the current SOLiD chemistry would do a little better & the current Illumina chemistry would do significantly better.

If there were more recently collected data analyzed in the same way, that would be very interesting to compare with these data.

[Joann]

SEQanswers Open?

Rather than depend on what shows up randomly in the published literature, could not this forum run a yearly "SEQanswers Open" on a standard template? This event could actually complement student lab training programs and promote platform understanding, excellence and standardized techniques among upcoming trainees.

[ECO]

Rather than depend on what shows up randomly in the published literature, could not this forum run a yearly "SEQanswers Open" on a standard template? This event could actually complement student lab training programs and promote platform understanding, excellence and standardized techniques among upcoming trainees.

This is interesting, but I'm not sure I get exactly what you mean. A yearly review of literature? A yearly benchmark of sequencer performance? A conference? Maybe this should be split out into a new thread?

[Heisman]

This is interesting, but I'm not sure I get exactly what you mean. A yearly review of literature? A yearly benchmark of sequencer performance? A conference? Maybe this should be split out into a new thread?

Honestly I think only once a year is too few considering how rapidly things are moving and the number of emerging technologies. Maybe twice a year?

[Joann]

Basically with reference to the literature above, groups (in training, even) could periodically run a standard template on their machine and properly report the data people want to see. Nothing fancy.

[james hadfield]

now that users can make barcoded libraries this could be done pretty easily. Someone just needs to make a big stock and send it out for free.

[ECO]

now that users can make barcoded libraries this could be done pretty easily. Someone just needs to make a big stock and send it out for free.

Good idea. I'd be up for it and or distributing/organizing...

[krobison]

Neat idea! I'd suggest a standard bacterial strain (E.coli DH10B?) as then all variants can be considered errors.

A related notion would be a place for people to post any standard dataset or even just some standard run statistics for their platforms.

[Corey]

now that users can make barcoded libraries this could be done pretty easily. Someone just needs to make a big stock and send it out for free.

I concur, this is a great idea. A little confused though about the best way to standardize a sample so that everyone is sequencing the same material. Is the idea to grow up and do a big E. coli (e.g. DH10B) genomic prep, have one or a few sites sequence this material and settle on a reference? Alternatively, to ensure everyone is sequencing the same fragments from the same reference, we could clone a library of a modest genome (maybe yeast is better that E. coli so there will not be any contaminating host DNA) and then distribute that library as DNA to anyone who asks? I'd be willing to make the library if anyone thinks it worthwhile. Not sure that the advantages of the latter approach outweigh its negatives.

[DZhang]

Rather than depend on what shows up randomly in the published literature, could not this forum run a yearly "SEQanswers Open" on a standard template? This event could actually complement student lab training programs and promote platform understanding, excellence and standardized techniques among upcoming trainees.

I think it is a great idea. Through reading some next-gen-related blogs, I came across a google-shared document:

https://spreadsheets0.google.com/spr...Lw&hl=en#gid=0.

We do not have to use it as is but the idea is there. Can we adopt a similar document/format on this site? I believe the next-related software wiki took a similar route. At the beginning, it is a bunch of threads and later there were structured ways to present, update, and organize information.

Douglas

https://www.contigexpress.com

[Seqasaurus]

regarding the actual subject of the thread, does anyone know where to get $-750 ion torrent sequencing? (see table 2)