---
Name: BBMap
URL: http://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
Description: >
	BBMap is a suite of pre-processing, assembly, alignment, and statistics
	tools for DNA/RNA sequencing reads.
---

The BBMap module produces summary statistics from the
[BBMap](http://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/) 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](http://seqanswers.com/forums/showthread.php?t=41057).
