I'm looking for an automated way to align multiple fasta files ~(50,000) to a custom made reference (fasta) and return the number of mismatched for each sequence. Each sequence and the reference are about 295 bp long. I have used bwa and bowtie to align sequences in the past but not sure if they can return the number of mismatches. I'm looking for a simplest way to accomplish this task.
Thanks your advice in advance