Current methods for aligning and identifying fungal ITS1 sequences are hampered by differences in aligning and identifying noncoding DNA with more established workflows for coding DNA such as 16s rRNA. This project makes use of existing command line tools to align ITS1 appropriately using local alignment alorithms and to trim non-ITS1 DNA from sequencing in pre-processing. I am currently expanding on the workflow to qualify the integrity of taxonomic assignments. While 97% similarity is a well established threshold for congeneric Bacteria, it doesn't work well for Fungi. Using the UNITE species hypothesis database, I am establishing appropriate thresholds for clusters of same-species, same-genus, etc. sequences to be used in downstream analysis.