##findSSRs_fastq_rawreads.pl This is an older script used to identify SSRs prior to an assembly. No primers are created. It looks through a fastq file.

##findSSRs_fasta.pl This is the new and improved SSR and primer calling script that should be used in all other circumstances.

##find_dup_begins.pl This script identifies forward and reverse reads with the same beginning bases. This is a problem we identified with some sets of paired end, overlapping (or supposed to be overlapping) reads. Seems limited to that one project.