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---
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).
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