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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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is Pilon OK with 454 data? #17

Closed dcopetti closed 7 years ago

dcopetti commented 8 years ago

Hello, I will have to polish and check the reliability of an assembly (I used Falcon and polished with Quiver), and the only short read data I have for this project is some 454 data (3 and 20 kb MP, single reads): will Pilon be OK with the 454 error model? Thanks, Dario

w1bw commented 8 years ago

Hi Dario,

It has been years since I've tried 454 data with Pilon. My worry would be that it could introduce spurious indel corrections, especially around homopolymer runs.

However, there's a good chance the next release will include the ability to control whether SNPs and Indels are corrected separately, that that might help for 454 data.

If you try it, take a look at the corrections Pilon makes and see whether they look right.

--bruce

On Tue, Aug 9, 2016 at 3:29 PM, dcopetti notifications@github.com wrote:

Hello, I will have to polish and check the reliability of an assembly (I used Falcon and polished with Quiver), and the only short read data I have for this project is some 454 data (3 and 20 kb MP, single reads): will Pilon be OK with the 454 error model? Thanks, Dario

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dcopetti commented 8 years ago

Thanks, I will test it again in the future with a new release.