Re: [wgs-assembler-users] Homopolymer error correction in CABOG

[Brian W. <th...@gm...>]

'CABOG' introduced support for a more sensitive overlap algorithm that was
insensitive to homopolymer errors, the 'mer' overlapper.  This did not
scale much past microbial assemblies, and is NOT recommended for use.
Aside from that, there was no explicit support for correcting homopolymer
errors.

Using sffToCA to convert from .sff to CA's .frg format will enable all the
454 specific algorithms.  Most of these deal with mate pairs.

b


On Thu, Jan 28, 2016 at 2:43 AM, Tamim Kabir <tam...@gm...> wrote:

> Dear Sir/Madam,
>
> Good day. We are assembling 454 (single + pair) end data for a plant
> genome by using CABOG. But, we are very much worried about homopolymer
> error of 454 data. How do we remove homopolymer error by using CABOG?
> What's parameter used I use for this purposes.
>
> Thanks in advance
> Shah Md Tamim Kabir
> Biotechnologist
> Dhaka, Bangladesh
>
>
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