any tool to join reads regardless of overlap?

Question

[from the mountains]

I'm hoping to find a tool that will merge reads if there's a non-ambiguous overlap, and join the rest of the reads with some symbol, like a number of hyphens or NNNNs. I vaguely remember finding a tool that can do it but now I can't remember. Help is appreciated!

[FatihSarigol]

Not sure I understand what you mean, but for merging paired reads for instance there is this tool https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmerge-guide/