Hello

This might be a stupid question, but I have just discovered tool called Breseq for microbial variant and SV analysis. The problem is that I have only paired end reads while breseq uses only single end reads. In their FAQ section they wrote this :
"Short answer: No.

Your reads are mapped in single-end mode even if you are using paired-end or mate-paired data. For most microbial genomes, you don’t gain much sensitivity (in terms of the number of reference positions at which there are enough uniquely-mapped reads to call mutations) by doing paired read mapping. Furthermore, the split-read analysis approach that breseq uses to discover new sequence junctions is more precise (finding exact sequence breakpoints) and generally at least as sensitive as predicting structural variation by examining read pairs that are mapped with anomalous orientations and insert sizes.

That said, there are definitely cases where this information can be useful, especially if one has data with large insert sizes (e.g. an Illumina mate paired library. So, we hope to include some of this functionality in the future. It just hasn’t been a very high priority."


So my question is: Can I use just one of the reads from paired end reads or is that huge mistake? Also could I use both of the reads and then compare the results? I would really need answers to this questions.

Thank you all in advance