bc_rarefy - Rarefy communities
bc_rarefy -input_files my_communities.generic \ -output_prefix my_converted_communities \ -sample_size 1000
This script reads a file containing biological communities and performs rarefaction, i.e. repeatedly takes a random subset of the community members, in order to normalize communities by member count. Rarefaction is useful to simulate an identical sampling effort for all communities. The output is a file containing rarefied, representative communities (integers). See Bio::Community::Tools::Rarefier for more information.
Input file containing the communities to rarefy. When providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files.
Path and prefix for the output files. Default: output_prefix.default
Number of members to randomly take at each bootstrap iteration. If omitted, the sample size defaults to the size (member count) of the smallest community.
Keep doing bootstrap iterations until the distance between the current average community and the average community at the previous iteration becomes less than the specified threshold. Default: dist_threshold.default
Perform the specified number of bootstrap iterations instead of a dynamic number of iterations based on a distance threshold. As a special case, use 'inf' to assume an infinite number of repetitions.
Write the average bootstraped communities (decimals) in addition to the rarefied communities (integers): 1 is yes, 0 is no. Default: write_average.default
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