Copy number (repeat count) of de nove assembly contigs

Question

[Caronkey]

I have a set of assembled contigs (genomic sequences). These contigs were assembled using a de novo short read assembler . I map/align the original reads data to these contigs using a short read mapper like bwa. So now I have a SAM/BAM alignment file at hand.

Is there any software (or a pipeline using different tools) to take this alignment SAM/BAM file as input and outputs which contigs are repeated in the genome and estimate those integer repeat counts (copy numbers) using coverage information in the alignment input file?

[lieven.sterck]

Might be me, but I'm a bit confused why you map new data to the assembly to get an idea on repeated contigs in your assembly? Why don't you align all contigs to themselves (eg. using minimap?) and extract that kind of info form that result?