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.
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.
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
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
Path and prefix for the output files. Default: output_prefix.default
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists.
Your participation is much appreciated.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: