I have looked through the documentation for BLAST command line tools and can't figure this out.
I have a set of long reads and I would like to find the accuracy of the reads. I am aligning the reads against the reference genome using BLAST.
However, very often BLAST will shorten a query read to get a better alignment, how can I force BLAST to only align the whole read? In the cases where the whole read does not align just create mismatches.
Thanks for your help.