There are some reads that just won't merge, especially if your fragments are longer than the combined read lengths. Try a tool like PEAR or BBMerge with relaxed settings, or skip merging and align as paired reads instead.
Yeah, like what the others said, it's common especially with varying read lengths or when the insert size distribution leads to situations where the reads don't fully overlap or have perfect complementarity in the overlap region. Tools like PEAR or FLASH should be able to handle this, and they often allow for some mismatches or an incomplete overlap when merging, while still trying to produce the longest possible contig. If you're getting overhangs or non-matching endings, it might indicate that your trimming was a bit aggressive, or that your merging parameters are too strict. You could try adjusting the minimum overlap required or allowing for a certain percentage of mismatches in the overlap region within your merging tool. Sometimes, you just can't perfectly merge everything, and it's okay to have some reads remain unmerged if they genuinely don't have sufficient overlap. I strongly recommend to focus on optimizing for the best possible outcome for the majority of your reads.
