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bbmap

The BBMap module produces summary statistics from the BBMap suite of tools. The module can summarise data from the following BBMap output files (descriptions from command line help output):

  • stats
    • BBDuk filtering statistics.
  • covstats (not yet implemented)
    • Per-scaffold coverage info.
  • rpkm (not yet implemented)
    • Per-scaffold RPKM/FPKM counts.
  • covhist
    • Histogram of # occurrences of each depth level.
  • basecov (not yet implemented)
    • Coverage per base location.
  • bincov (not yet implemented)
    • Print binned coverage per location (one line per X bases).
  • scafstats (not yet implemented)
    • Statistics on how many reads mapped to which scaffold.
  • refstats
    • Statistics on how many reads mapped to which reference file; only for BBSplit.
  • bhist
    • Base composition histogram by position.
  • qhist
    • Quality histogram by position.
  • qchist
    • Count of bases with each quality value.
  • aqhist
    • Histogram of average read quality.
  • bqhist
    • Quality histogram designed for box plots.
  • lhist
    • Read length histogram.
  • gchist
    • Read GC content histogram.
  • indelhist
    • Indel length histogram.
  • mhist
    • Histogram of match, sub, del, and ins rates by read location.
  • statsfile (not yet implemented)
    • Mapping statistics are printed here.

Additional information on the BBMap tools is available on SeqAnswers.