Florent Angly > Bio-Community > bc_clean_shrapnel

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NAME ^

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

SYNOPSIS ^

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

DESCRIPTION ^

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.

REQUIRED ARGUMENTS ^

-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.

OPTIONAL ARGUMENTS ^

-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

FEEDBACK ^

Mailing Lists

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

Reporting Bugs

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:

  http://bugzilla.open-bio.org/

AUTHOR - Florent Angly ^

Email florent.angly@gmail.com

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