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.