What is the best tool for computing the overlaps between each read in a set of short reads?
For example, I have a set of reads from an RNA-Seq project, and for a specific read from that set of reads, I'd like to find all the reads that overlap significantly with the chosen read.
It must be also noted that I'm doing this de novo, so no reference is available.
I don't know if BLAST's fast enough for this task, because in my past experience with BLAST it seems rather slow.
I've seen this paper, but I'd like something such as Bowtie or BWA, but I haven't found such a tool.