how to align concatenated and sheared sequences?

[Lilach]

Hi,

I enriched DNA targets by PCR, them concatenated (ligated) the DNA and sheared it to get ~300 bp sequences.
The problem is that each read may include sequences from two different genomic regions.
The sequencing was performed with HiSeq PE x 100.
How can I do the alignment with free software?

In regular enrichments (RNA hybridization) I'm just using bwa and samtools, but I don't know if it is suitable for this case as well?

Thanks,
Lilach

[swbarnes2]

I think that's going to be ugly; with short reads, you need speed, and you can't break apart 100 Mreads a thousand ways each to see how the two ends might best map on separate reference sequences.

You could try making concatenated reference sequence for those reads to align to.

[Lilach]

Thanks for the answer, although I hope there will be an easier way...
I know what will be the PCR products. Is there any efficient algorithm that can concatenate these known sequences in all possible ways and "break" to pieces, to see what I get? Then I could align my results to this database?
But I still have to "label" somehow each PCR product before the concatenation to know where it came from? or at least where are the end points or original sequences?