|
0
|
1 Trimmomatic
|
|
|
2 ===========
|
|
|
3
|
|
|
4 XML tool file and shell script wrapper for the Trimmomatic program, which provides
|
|
|
5 various functions for manipluating Illumina FASTQ files.
|
|
|
6
|
|
|
7 Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university:
|
|
|
8
|
|
|
9 * <http://www.usadellab.org/cms/index.php?page=trimmomatic>
|
|
|
10
|
|
|
11 The reference for Trimmomatic is:
|
|
|
12
|
|
|
13 * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a
|
|
|
14 user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
|
|
|
15 Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7)
|
|
|
16
|
|
|
17 Trimmomatic 0.32 can be obtained from:
|
|
|
18
|
|
|
19 * <http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip>
|
|
|
20
|
|
|
21 The tool assumes that two environment variables have been set, in order to find the
|
|
|
22 appropriate files:
|
|
|
23
|
|
|
24 * `TRIMMOMATIC_DIR` should point to the directory holding the
|
|
|
25 `trimmomatic-0.32.jar` file, and
|
|
|
26
|
|
|
27 * `TRIMMOMATIC_ADAPTERS_DIR` should point to the directory holding the adapter
|
|
|
28 sequence files (used by the `ILLUMINACLIP` option).
|
|
|
29
|
|
|
30 Both variables will be set automatically if installing the tool dependencies e.g. via
|
|
|
31 a toolshed; otherwise they will need to be set manually in the Galaxy environment.
|
|
|
32
|
|
|
33 To add to Galaxy add the following to tool_conf.xml:
|
|
|
34
|
|
|
35 <tool file="trimmomatic/trimmomatic.xml" />
|
|
|
36
|
|
|
37 (The tool no longer uses a `.loc` file to point to the location of the adapter
|
|
|
38 sequence files)
|
|
|
39
|
|
|
40 ### Changes ###
|
|
|
41
|
|
|
42 0.32.1: Remove `trimmomatic_adapters.loc.sample` and hard-code adapter files into
|
|
|
43 the XML wrapper.
|
|
|
44
|
|
|
45 0.32.0: Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and
|
|
|
46 (set the environment). Update tool versioning to use Trimmomatic version
|
|
|
47 number (i.e. `0.32`) with tool iteration appended (i.e. `.1`).
|
|
|
48
|
|
|
49 0.0.4: Specify '-threads 6' in <command> section.
|
|
|
50
|
|
|
51 0.0.3 : Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
|
|
|
52
|
|
|
53 0.0.2: Updated ILLUMINACLIP option to use standard adapter sequences (requires the
|
|
|
54 trimmomatic_adapters.loc file; sample version is supplied) plus cosmetic
|
|
|
55 updates to wording and help text for some options.
|
|
|
56
|
|
|
57 0.0.1: Initial version
|
