BBMap

Description

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.

File search patterns

bbmap/stats:
  contents: "#Name\tReads\tReadsPct"
  num_lines: 4
bbmap/aqhist:
  contents: "#Quality\tcount1\tfraction1\tcount2\tfraction2"
  num_lines: 1
bbmap/bhist:
  contents: "#Pos\tA\tC\tG\tT\tN"
  num_lines: 1
bbmap/bincov:
  contents: "#RefName\tCov\tPos\tRunningPos"
  num_lines: 3
bbmap/bqhist:
  contents: "#BaseNum\tcount_1\tmin_1\tmax_1\tmean_1\tQ1_1\tmed_1\tQ3_1\tLW_1\tRW\
    _1\tcount_2\tmin_2\tmax_2\tmean_2\tQ1_2\tmed_2\tQ3_2\tLW_2\tRW_2"
  num_lines: 1
bbmap/covhist:
  contents: "#Coverage\tnumBases"
  num_lines: 1
bbmap/covstats:
  contents: "#ID\tAvg_fold"
  num_lines: 1
bbmap/ehist:
  contents: "#Errors\tCount"
  num_lines: 1
bbmap/gchist:
  contents: "#GC\tCount"
  num_lines: 5
bbmap/idhist:
  contents: "#Mean_reads"
  num_lines: 1
bbmap/ihist:
  contents: "#InsertSize\tCount"
  num_lines: 6
bbmap/indelhist:
  contents: "#Length\tDeletions\tInsertions"
  num_lines: 1
bbmap/lhist:
  contents: "#Length\tCount"
  num_lines: 1
bbmap/mhist:
  contents: "#BaseNum\tMatch1\tSub1\tDel1\tIns1\tN1\tOther1\tMatch2\tSub2\tDel2\t\
    Ins2\tN2\tOther2"
  num_lines: 1
bbmap/qahist:
  contents: "#Deviation"
  num_lines: 1
bbmap/qchist:
  contents_re: "#Quality\tcount1\tfraction1\\n"
  num_lines: 1
bbmap/qhist:
  contents: "#BaseNum\tRead1_linear\tRead1_log\tRead1_measured\tRead2_linear\tRea\
    d2_log\tRead2_measured"
  num_lines: 1
bbmap/rpkm:
  contents: "#File\t"
  num_lines: 1
bbmap/statsfile_machine:
  contents: Reads Used=
  num_lines: 1
bbmap/statsfile:
  contents: "Reads Used:"
  num_lines: 1