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

[Sebastian J. <sja...@Ce...>]

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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