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diff --git a/hwg_gssr_scripts/README.md b/hwg_gssr_scripts/README.md
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+##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.
+
diff --git a/hwg_gssr_scripts/findSSRs_fastq.pl b/hwg_gssr_scripts/findSSRs_fastq_rawreads.pl
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rename from hwg_gssr_scripts/findSSRs_fastq.pl
rename to hwg_gssr_scripts/findSSRs_fastq_rawreads.pl