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BBDuk

Common data-quality-related trimming, filtering, and masking operations with a kmer based approach

https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/

The module produces summary statistics from the stdout logging information from the BBDuk tool of the BBTools suite of tools.

"Duk" stands for Decontamination Using Kmers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool.

The module can summarise data from the following BBDuk funtionality (descriptions from command line help output):

  • entropy - entropy filtering
  • ktrim - kmer trimming
  • qtrim - quality trimming
  • maq - read quality filtering
  • ref contaminant filtering

Additional information on the BBMap tools is available on SeqAnswers.

File search patterns​

bbduk:
  contents: Executing jgi.BBDuk
  num_lines: 2