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Old 03-11-2009, 10:53 AM   #21
RudyS
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Roald

I am using CLC Genomics Workbench 3 ... is this already outdated considering your posting here:

"We have just included native color space assembly in our NGS Cell software"

... I have some "issues" with the lack of connectivity of denovo contigs with WB3 ... i mean, the reads are there, but from what i am seeing WB3 is too finicky ... have been in touch with your colleagues in Denmark, but my "issues" pile up faster than their responses

would the new algorithm in the NGS Cell software improve my results? should people be buying that instead of the WB3?

RudyS
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Old 03-19-2009, 02:53 AM   #22
Roald
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Hi RudyS,

Thank you for your interest.

We are now at version 3.2 with the Genomics Workbench and I recommend you to get the updated version if you have not done so already.
At the moment we are working on a number of improvements, amongst which is de novo assembly in color space, so stay tuned for that.
If you write me a personal message with the details, I will be happy to look into your support issues.

Regarding the NGS Cell, the algorithms and data structures used are the same as those within the Workbench. The Cell just offers these in a command line environment, suited for integration into a pipeline in a scripting environment.

Hope this helps.

Cheers

Roald
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Old 04-21-2009, 12:14 AM   #23
nilshomer
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We have used BFAST for own alignment purposes (admittedly I am the author). We have don't use "valid adjacent" rules (i.e. heuristic), but a full dynamic programming algorithm (equivalent to solving a shortest path dag or HMM) to identify errors, SNPs and indels. I don't believe that other aligners (beyond SHRiMP) support alignment with indels, but I may be mistaken.

Finally, if there is a sequencing error (color error), without proper identification of the error (some would call this correction), all decoded bases after the color will be mismatches compared to the reference (or true underlying sequence). This is why you cannot use other alignment tools, since the truly you are dealing with encoded bases, which rely on a reference to identify errors. Now consider more difficult situations, where there is truly a variant (SNP) and a color error occurs in the first color encoding the variant. Similarly, there can be the pattern error, match, error which is equally likely to be a variant (SNP) and an error, but what do we prefer? It gets complicated, so I would instead use an aligner that supports color space (MAQ, Bowtie, BFAST, SHRiMP) so that you do not have to modify alignment algorithms.
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