Re: [wgs-assembler-users] High ReadsWithBothDegenMate, use de novo classifier (DNC)?

[Ole K. T. <o.k...@bi...>]

Hi Sebastian.
I'm not completely sure I understand what you want, but dNC is part of CA 7.0.
As far as I understand, this is how you use it. Put this in your spec file:
dncMPlibraries = shortjump
dncBBlibraries = frag
where "shortjump" is the name of your mate pair library, your Illumina
library in this case,  and "frag" is the name of a library it will
compare with to find PE reads, I think your 454 reads will work fine
here.

Good luck!

Ole

On 16 February 2012 15:58, Sebastian Jaenicke
<sja...@ce...> wrote:
> Hi,
>
> I'm trying to assemble a bacterial genome based on 454 (WGS) and
> Illumina (PE) data with WGS 7.0; however, I'm seeing a large number
> of degenerated mate pairs ('ReadsWithBothDegenMate', up to 85%
> of the Illumina data).
>
> I'd like to use DNC to verify the PE distance, but according to
> http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Pair_classification_within_Illumina_mate_pair_data
> the DNC software should be part of the WGS 7.0 release, but seems
> to be missing.
>
> Any hints?
>
> Regards,
>
> - Sebastian
>
> --
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