Florent Angly
and 1 contributors


bc_clean_shrapnel - Remove low-count, low-prevalence community members


  bc_clean_shrapnel -input_files          communities.generic         \
                    -count_threshold      1                           \
                    -prevalence_threshold 1                           \
                    -output_prefix        cleaned_communities.generic


This script takes communities, removes shrapnel (low abundance, low prevalence members that are likely to be the result of sequencing errors) and saves the resulting communities in output files. By default, the cleaner removes only singletons, i.e. community members that appear in only one community (prevalence of 1) and have only 1 count. You can specify your own count and prevalence thresholds though. See Bio::Community::Tools::ShrapnelCleaner for more information.


-if <input_files>... | -input_files <input_files>...

Input file containing the communities to process. When providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files.


-ct <count_threshold> | -count_threshold <count_threshold>

Provide a count threshold for shrapnel removal. Community members with a count equal or lower than this threshold are removed (provided they also meet <prevalence_threshold>). Default: count_threshold.default

-pt <prevalence_threshold> | -prevalence_threshold <prevalence_threshold>

Provide a prevalence threshold for singleton removal. Community members with a prevalence (number of communities that the member is found in) equal or lower than this threshold are removed (provided they also meet the count_threshold). Default: prevalence_threshold.default

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. Default: output_prefix.default


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AUTHOR - Florent Angly

Email florent.angly@gmail.com