There are probably serious bugs in all sequence alignment software, but it's unclear how much it does matter. Downstream analysis must assume that the alignment

There are probably serious bugs in all sequence alignment software, but it's unclear how much it does matter. Downstream analysis must assume that the alignments contain all kinds of known and unknown errors anyway. The sequence alignment problem itself is so ill-defined and there are so many sources of bias and errors, from data to algorithms, from code to reference sequences, from instruments to sample preparation, and including your definition of truth, that you often can't say confidently whether the alignment is correct. The scale of the data is often also big enough that you have to make deliberate trade-offs between costs and correctness.