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Complete documentation on how to run SuperCRUNCH is available at: https://github.com/dportik/SuperCRUNCH/wiki The following generalized commands were used to run the analysis. Please note that the `/Path/To/` should be changed to the actual file locations. The contamination filter was run to identify human sequences in the mtDNA markers. This is a similar analysis to reference-based similarity searching, but with removal of bad sequences. The required reference files and keys are included in the inputs folder in this module. ``` python Contamination_Filter.py -i /Path/To/4c-Contamination/input -o /Path/To/4c-Contamination/output --multisearch /Path/To/4c-Contamination/multisearch-key-contam.txt -b dc-megablast ``` This analysis identified 3 bad sequences, 1 for 12S and 2 for 16S.
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