BBTools

Pre-processing, assembly, alignment, and statistics tools for DNA/RNA sequencing reads

http://jgi.doe.gov/data-and-tools/bbtools/

The 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/aqhist:
  contents: "#Quality\tcount1\tfraction1\tcount2\tfraction2"
  num_lines: 10
bbmap/bhist:
  contents: "#Pos\tA\tC\tG\tT\tN"
  num_lines: 10
bbmap/bincov:
  contents: "#RefName\tCov\tPos\tRunningPos"
  num_lines: 10
bbmap/bqhist:
  contents: "#BaseNum\tcount_1\tmin_1\tmax_1\tmean_1\tQ1_1\tmed_1\tQ3_1\tLW_1\tRW_1\t\
    count_2\tmin_2\tmax_2\tmean_2\tQ1_2\tmed_2\tQ3_2\tLW_2\tRW_2"
  num_lines: 10
bbmap/covhist:
  contents: "#Coverage\tnumBases"
  num_lines: 10
bbmap/covstats:
  contents: "#ID\tAvg_fold"
  num_lines: 10
bbmap/ehist:
  contents: "#Errors\tCount"
  num_lines: 10
bbmap/gchist:
  contents:
    - "#Mean\t"
    - "#GC\tCount"
  num_lines: 10
bbmap/idhist:
  contents:
    - "#Mean_reads"
    - "#Identity\tReads\tBases"
  num_lines: 10
bbmap/ihist:
  contents:
    - "#Mean\t"
    - "#InsertSize\tCount"
  num_lines: 10
bbmap/indelhist:
  contents: "#Length\tDeletions\tInsertions"
  num_lines: 10
bbmap/lhist:
  contents: "#Length\tCount"
  num_lines: 10
bbmap/mhist:
  contents: "#BaseNum\tMatch1\tSub1\tDel1\tIns1\tN1\tOther1\tMatch2\tSub2\tDel2\t\
    Ins2\tN2\tOther2"
  num_lines: 10
bbmap/qahist:
  contents: "#Quality\tMatch\tSub\tIns\tDel"
  num_lines: 10
bbmap/qchist:
  contents_re: "#Quality\tcount1\tfraction1$"
  num_lines: 10
bbmap/qhist:
  contents: "#BaseNum\tRead1_linear\tRead1_log\tRead1_measured"
  num_lines: 10
bbmap/rpkm:
  contents:
    - "#File\t"
    - "#Reads\t"
    - "#Mapped\t"
    - "#RefSequences\t"
    - "#Name Length"
  num_lines: 10
bbmap/stats:
  contents:
    - "#File"
    - "#Total"
    - "#Matched"
    - "#Name\tReads\tReadsPct"
  num_lines: 10
bbmap/statsfile:
  contents:
    - "Reads Used:"
    - "Mapping:"
    - "Reads/sec:"
    - "kBases/sec:"
  num_lines: 10
bbmap/statsfile_machine:
  contents: Reads Used=
  num_lines: 10