I am experimenting with BowTie v 1 for various length reads (75 to 200 bp). Now, my task is to find it's throughput and accuracy. But, I can't understand how to find it's accuracy. Now, I was suggested to use an fully accurate tool and compare it to BowTie in-order to find accuracy. Can anybody help me, is there any other method (because that is really time consuming work) ? Or if I must have to compare BowTie with another tool, can anybody help me which tool I can use for above purpose. Thanks in advance.
NB: BowTie uses only substitution for finding mismatch.