Selection of minimum score parameter for bowtie2 based on known composition of mock communities.
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(A) Setting the Bowtie2 scoring minimum set to “Local G,80,8”, where 80 is the base score added to the scaling formula, produced mapping proportions with the least deviation from expected for both mock communities, out of the range of values tested. (B) Observed and expected proportions for the Mock1 community. (C) Observed and expected proportions for the Mock2 community.