1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
---
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).
|
