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Old 07-23-2009, 03:16 AM   #1
dan
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Default Best tool to map 454 reads onto sanger reads?

I have some very low coverage Sanger sequencing data for a small genome that I would like to try to 'expand' using a higher coverage 454 data set.

Should I just assemble the 454 reads and map the Sanger sequences onto the contigs?

Any advantage in trying to map the 454 reads onto the Sanger reads?

Cheers,
Dan.
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Old 07-23-2009, 10:38 AM   #2
hlu
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I suppose that you are trying to do assembly.

The 454 GS Assembler (newbler) software support hybrid assembly with Sanger + 454 data. You could do one big assembly including all the Sanger and 454 data.
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Old 07-25-2009, 12:51 PM   #3
BaCh
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Quote:
Originally Posted by dan View Post
Should I just assemble the 454 reads and map the Sanger sequences onto the contigs?
Any advantage in trying to map the 454 reads onto the Sanger reads?
Unless your existing Sanger consensus hasn't been the work of weeks or months of manual contig joining and finishing, you probably want to do a full de-novo assembly with both the Sanger and the 454 reads.

I'd take either MIRA (because it has tagging features which point to differences between sequencing technologies) or CABOG for de-novo assembly of 454 and Sanger. Something important to notice: if the DNA used to do the Sanger sequencing and the 454 sdequencing is not 100% the same, you will find some differences between Sanger and 454 which cannot be explained by sequencing errors. Those would be real.

If you really just want to map to your existing reference, MIRA will also do this happily and even point out all the places where there are differences.

Regards,
B.

PS: Disclaimer: I'm biased regarding MIRA, it's my baby See http://chevreux.org/mira_ex_454sanger.html for an example how a Sanger / 454 hybrid de-novo looks
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Old 07-27-2009, 08:51 AM   #4
dan
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PS: Disclaimer: I'm biased regarding MIRA, it's my baby See http://chevreux.org/mira_ex_454sanger.html for an example how a Sanger / 454 hybrid de-novo looks
Great! Then you're the person to ask... Which is better, MIRA or CABOG? ;-)

Thanks very much for the infomation above, I'll let you know how I get on.

Dan.
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