assembly improvement based on gene set - is any tool for this?

[paraslonic]

Hi!
Do you know some tool which can find misassembly events based on references or set of reference genes?

I find that about 8% of genes in Ion Torrent assemblies of E. coli have frameshifts or gain of stop codons. None of the reference (from nr blast db) has such variants so I suppose it`s a false variants due to torrent non-random errors.

I think we can change assembly based references (genes or genomes) if in some proportion of the reads are supporting reference variants.

Is such soft (or something like) exists?

The only tool I find is GeneStitch, though it`s primary use for metagenomics and user need to assemble genomes with SOAP...

Thank for sharing info,
best regards,
Aleksander Manolov