GenomeQuest 6.0 beta

[GenomeQuest]

Dear all,

Just a brief message to point you also to GenomeQuest's new beta offering in NGS sequence data management and analysis. I think the offering is pretty exciting and may be valuable for researchers and bioinformaticists. For you to decide...

You can try it for free with no obligation: www.genomequest.com. It runs in your web browser.

Currently we support RNA-Seq, Variant calling, Rapid Annotation (metagenomics), and long read assembly, as well as high-throughput mapping. CHiP-Seq, micro RNA, other assembly tools, and much more will be rolled out shortly. All of the world's reference data is kept up to date inside the system so you get up-to-the-minute accuracy. And you can upload and use your own reference data if you prefer. Of course, there are APIs for bioinformaticists to extend and integrate the system, and we're about to release a huge update to the APIs that make it stronger still. Again, much much more to come in the coming weeks and months. I'll let it speak for itself.

Most importantly, we're looking for your detailed help to make it better. We have a linkedin group for feature requests athttp://www.linkedin.com/groups?gid=2056733 and I'd welcome any comments you have directly via email, as well.

Thanks for letting me have the opportunity to announce the new product.

Best regards,
Richard
[email protected]

[nilshomer]

Dear all,

Just a brief message to point you also to GenomeQuest's new beta offering in NGS sequence data management and analysis. I think the offering is pretty exciting and may be valuable for researchers and bioinformaticists. For you to decide...

You can try it for free with no obligation: www.genomequest.com. It runs in your web browser.

Currently we support RNA-Seq, Variant calling, Rapid Annotation (metagenomics), and long read assembly, as well as high-throughput mapping. CHiP-Seq, micro RNA, other assembly tools, and much more will be rolled out shortly. All of the world's reference data is kept up to date inside the system so you get up-to-the-minute accuracy. And you can upload and use your own reference data if you prefer. Of course, there are APIs for bioinformaticists to extend and integrate the system, and we're about to release a huge update to the APIs that make it stronger still. Again, much much more to come in the coming weeks and months. I'll let it speak for itself.

Most importantly, we're looking for your detailed help to make it better. We have a linkedin group for feature requests athttp://www.linkedin.com/groups?gid=2056733 and I'd welcome any comments you have directly via email, as well.

Thanks for letting me have the opportunity to announce the new product.

Best regards,
Richard
[email protected]

Any benchmarks for mapping or assembly, or comparisons to known algorithms for mapping or assembly? Is it a new algorithm (to be published) or an existing one? Thanks for letting us know!

[GenomeQuest]

About our HS3 algorithm

Hi there. At GenomeQuest we have a long standing tradition of algorithm design and optimization (10+ years, and our own algorithm development team).

The HS3 algorithm is derived from work that has been published already in 2002 (see reference below). This algorithm tries to align the entire (short) read to the reference, allowing mismatches and / or gaps. Currently for Illumina reads we use two mismatches or gaps in most of our workflows, but this is configurable and there is no performance penalty in asking for more. We use a simple statistics approach to select those reads we trust are mapped to the right position (functionally equivalent to MAQ's mapping score). HS3 handles Solexa, Solid (in colorspace) and 454 reads. For longer reads we can also opt for a local alignment strategy (that very much resembles Smith & Waterman, or even BLAST itself).

We have never really systematically compared the speed of our algorithms to everything else out there. All I can say is that I don’t find (expect) it to be very different. We have looked at the quality of our alignments compared to others, however. Our algorithm doesn't take any heuristic short cuts and finds mismatches and indels. If you have spent months planning and running a biological experiment, then you can wait a few extra hours to get the most accurate analysis (and not have to validate numerous alignment artifacts in the wet lab, and even miss out on real results). We decided that for a biologist accuracy matters much more than speed.

As well, all sequence comparison algorithms in our core engine toolbox (20+ algorithms) run multiple threads / multiple nodes, and scale very well without huge memory requirements. This means that performance can easily be improved simply by allocating more hardware for the problem. You don't even have to buy it / manage it yourself if you don't want to, because you can make use of our (500+ cores and growing) cloud.

I hope this helps.
Regards, Henk Heus (Senior scientific consultant, GenomeQuest).

Proc IEEE Comput Soc Bioinform Conf. 2002;1:228-36. High similarity sequence comparison in clustering large sequence databases. Dudoignon L, Glemet E, Heus HC, Raffinot M.

[GenomeQuest]

Forgot to say

I forgot to say that at GenomeQuest we understand that we can not be on top of everything all of the time. Therefore our platform is designed in such a way that other algorithms and software can be plugged in (easily) through various API layers and plugin systems. This way, you will benefit from all the other goodies within the platform (reference data, web interface, reporting and sharing results, etc) and still run your favorite software. We have done this for newbler, velvet, and a host of other useful software. It's not difficult to do this yourself.

Henk Heus (GenomeQuest)

[GenomeQuest]

We'd Like To Hear From You: Take The NGS Survey

Please share your views on next generation sequencing, in a survey at www.genomequest.com <http://www.genomequest.com> ....see "Take the NGS Survey" on the top right of the home page.

We’ll share the results.

Thank you for your time and participation.

Best regards,
Richard
[email protected]