Denovo assembly between PCR primers.

[marcovth]

Hello ...

Is there an open source NGS assembler available which "trace-walks" between Multiplex PCR primers?

I want to use a number of 5' primers and one single 3' primer per barcode for Multiplex PCRs.

I would like the assembler to start "trace walking" from any of the 5' primers, generating a denovo assembly, until it reaches the 3' primer (or stops at a certain max assembly length).

The reads used for the assembly started by one 5' primer, should also be available for the assembly started by any of the other 5' primers.

Is anything like this available for a command-line pipe-line?

I have been searching for a number of days for the right solution.

Thanks in advance for any suggestions.