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Old 03-04-2010, 12:24 AM   #1
strob
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Default sequencing technologies overview

Dear all,

after attending the AGBT2010 meeting, I made this list of potential sequencing technologies out there. Is this list complete?

1. illumina (Avantome, GAIIx, HisSeq2000) (http://www.illumina.com/applications/sequencing.ilmn)
2. Roche (454 Genome Sequencer FLX, GS Junior) (http://454.com/products-solutions/45...-portfolio.asp)
3. Life Technologies (SOLiD, Single Molecule Sequencing) (http://www.lifetechnologies.com/sequencing.html)
4. Helicos (True Single Molecule Sequencing) (http://www.helicosbio.com/)
5. Pacific Biosciences (Real Time Single Molecule Sequencing) (http://www.pacificbiosciences.com/)
6. Ion Torrent (Post-Light Sequencing™ technology) (http://www.iontorrent.com/)
7. Oxford nanopore (Single Molecule Sequencing) (http://www.nanoporetech.com/)
8. IBM nanopore sequencing (Single Molecule Sequencing) (http://www-03.ibm.com/press/us/en/pr...ease/28558.wss)
9. Nabsys (nanopore + electronic sequencing) (http://www.nabsys.com/)
10. ZS Genetics (http://www.zsgenetics.com/)
11. Visigen (http://genomics.xprize.org/teams/vis...chnologies-inc)
12. Halcyon Molecular (http://www.halcyonmolecular.com/)
13. Complete Genomics (only human till now) (http://www.completegenomics.com/)
14. Mobious (Nexus I) (http://www.mobious.com/mobious_produ...18/page18.html)
15. Polonator (MPS by ligation) (http://www.polonator.org/)
16. Cracker (SMRT on a chip) http://www.crackerbio.com/
17. Kavli Institute of Nanoscience; Graphene Nanopores (http://arxiv.org/ftp/arxiv/papers/1005/1005.4754.pdf)
18. ...

Hope this could be helpful,

Steven

Last edited by strob; 05-31-2010 at 11:40 PM.
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Old 03-04-2010, 12:39 AM   #2
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Quote:
Originally Posted by strob View Post
Dear all,

after attending the AGBT2010 meeting, I made this list of potential sequencing technologies out there. Is this list complete?

1. illumina (GAIIx, HisSeq2000) (http://www.illumina.com/applications/sequencing.ilmn)
2. Roche (454 Genome Sequencer FLX, GS Junior) (http://454.com/products-solutions/45...-portfolio.asp)
3. Life Technologies (SOLiD, Single Strand Sequencing) (http://www.lifetechnologies.com/sequencing.html)
4. Helicos (Single Strand Sequencing) (http://www.helicosbio.com/)
5. Pacific Biosciences (Real Time Single Strand Sequencing) (http://www.pacificbiosciences.com/)
6. Ion Torrent (Single strand Sequencing) (http://www.iontorrent.com/)
7. Oxford nanopore (Single Strand) (http://www.nanoporetech.com/)
8. IBM nanopore sequencing (Single Strand) (http://www-03.ibm.com/press/us/en/pr...ease/28558.wss)
9. Nabsys (nanopore + electronic sequencing) (http://www.nabsys.com/)
10. ZS Genetics (http://www.zsgenetics.com/)
11. Visigen (http://genomics.xprize.org/teams/vis...chnologies-inc)
12. Halcyon Molecular (http://www.halcyonmolecular.com/)
13. Complete Genomics (only human till now) (http://www.completegenomics.com/)
14. ...?

Hope this could be helpful,

Steven
http://www.bionanomatrix.com/
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Old 03-04-2010, 12:43 AM   #3
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I thought that Bionanomatrix only provides chips to line up the DNA, but they don't do any sequencing themselves...
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Old 03-04-2010, 05:34 AM   #4
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Default AGBT 2010 sequencing technology summary

Complete Genomics (http://www.completegenomics.com/) provides large-scale sequencing of human genomes as a service. Its focus hasn't changed.
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Old 03-04-2010, 05:37 AM   #5
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that's why they are number 13 in my list (speaking as a plant scientist) ;-)
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Old 03-04-2010, 05:39 AM   #6
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Ah, wishful thinking then!
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Old 03-04-2010, 07:13 AM   #7
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What do you all think, is it time to expand "The Pipeline" forum into more companies (the list above being a great start)?

My rule was previously that you had to have a commercially released instrument, but I think there is definitely room for more discussion that one forum allows.

Thoughts?
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Old 03-04-2010, 07:46 AM   #8
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I think Complete Genomics is best served with the Service Providers forum. How about a "single molecule sequencing" forum.

PS Ion Torrent isn't single strand sequencing.
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Old 03-04-2010, 07:50 AM   #9
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indeed, I adjusted the list: Ion Torrent (Post-Light Sequencing™ technology)

Thanks
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Old 03-04-2010, 07:55 AM   #10
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"Single Molecule" I think is what you're looking for vs. "single strand"
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Old 03-04-2010, 12:18 PM   #11
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@ECO: yes, why not have the Pipeline for "those that either have a commercially released instrument, or are well on their way". I guess you can be the judge, and we'll protest if we don't agree a certain system falls under the definition :-)
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Old 03-04-2010, 01:20 PM   #12
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Some additions to the list:

* Mobious: Nexus I
http://www.mobious.com/mobious_produ...18/page18.html
* Illumina: Avantome (pyrosequencing)
* Polonator (MPS by ligation)
* Cracker (SMRT on a chip) http://www.crackerbio.com/
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Old 03-04-2010, 03:45 PM   #13
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Quote:
Originally Posted by ECO View Post
What do you all think, is it time to expand "The Pipeline" forum into more companies (the list above being a great start)?

My rule was previously that you had to have a commercially released instrument, but I think there is definitely room for more discussion that one forum allows.

Thoughts?
I would wait and see what's the number of questions each new platform gets. As soon as we see some traffic then you can create specific Forums.
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Old 03-04-2010, 09:13 PM   #14
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Quote:
Originally Posted by flxlex View Post
@ECO: yes, why not have the Pipeline for "those that either have a commercially released instrument, or are well on their way". I guess you can be the judge, and we'll protest if we don't agree a certain system falls under the definition :-)
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I would wait and see what's the number of questions each new platform gets. As soon as we see some traffic then you can create specific Forums.
One vote for, one vote against. Need more input.

I think it would be a good opportunity to clearly lay out the technical summaries of each company...like I did so long ago on the Next Gen Summaries page.
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Old 03-04-2010, 09:17 PM   #15
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Quote:
Originally Posted by ECO View Post
One vote for, one vote against. Need more input.

I think it would be a good opportunity to clearly lay out the technical summaries of each company...like I did so long ago on the Next Gen Summaries page.
I am in favor of adding them by request (by users or vendors). It looks like there are a lot of companies/technologies and it would get cluttered quickly if a forum existed for each one before there are users/vendors who would post to the site.
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Old 03-04-2010, 11:17 PM   #16
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I updated and modified the list

Many thanks for all the input!!!
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Old 03-09-2010, 12:46 PM   #17
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Quote:
Originally Posted by nilshomer View Post
I am in favor of adding them by request (by users or vendors). It looks like there are a lot of companies/technologies and it would get cluttered quickly if a forum existed for each one before there are users/vendors who would post to the site.
I agree. Thats a good balance to avoid clutter, and at the same time remain open for the new ones..
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Old 03-09-2010, 02:28 PM   #18
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What about querying the database to see the number threads per technology. If > X we create a forum.

Opening them by user/vendor request sounds fine to me too.
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Old 03-12-2010, 06:57 PM   #19
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Good suggestions all. I'll keep an eye out for too much discussion about any single vendor overwhelming this forum, or for new instrument releases. Thanks.
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Old 04-05-2010, 08:11 AM   #20
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Congratulations to Strob for this very useful list and for the working links. This is very helpful and informative, good work!
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