Merge paired end reads without overlap

Question

[ahramkim1128]

I did PCR for NGS analysis with ~400bp. Since 5' and 3' regions of 400bp were important to me, I just sequenced both region with 150bp length without sequencing the middle of PCR products. I received the sequencing data (fastq) that contain both paired end reads in a single fastq.

I'd like to merge paired-end reads into single line (?) and proceed BlastX analysis of merged DNA sequences with my interest protein sequence. When I used merging tools that use overlap strategy to match paired end reads, I lost many sequence data.

Is there a good tool that doesn't need the overlap region to merge paired end reads in a single file?

Thanks,