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author iuc
date Wed, 24 Jan 2024 08:56:01 +0000
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1 Trimmomatic: flexible read trimming tool for Illumina NGS data
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2 ==============================================================
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3
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4 Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
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5 manipluating Illumina FASTQ files (both single and paired-end).
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6
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7 Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university
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8 http://www.usadellab.org/cms/index.php?page=trimmomatic
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9
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10 The reference for Trimmomatic is:
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11
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12 - Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
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13 for Illumina Sequence Data. Bioinformatics, btu170.
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15 Controlling the available memory
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16 ================================
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18 The default amount of memory avilable to trimmomatic is set to 8GB.
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19 To change the default amount of memory you can set the environment variable
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20 ``_JAVA_OPTIONS`` to ``-Xmx<amount_of_memory_in_GB>G``. The recommended way to
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21 set this is in the job_conf.xml file. To change the available memory to 6GB, a
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22 line like the below should be added:
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24 ``<env id="_JAVA_OPTIONS">-Xmx6G</env>``
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26 This will set the environment variable ``_JAVA_OPTIONS`` to ``-Xmx6G``.
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27
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28 History
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29 =======
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30
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31 ============== ================================================================
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32 Version Changes
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33 -------------- ----------------------------------------------------------------
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34 0.39+galaxy1 - Relocated to the ``tools-iuc`` repository
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35 0.39 - Update to Trimmomatic 0.39.
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36 0.38.1 - Bug fix: add dependency on ``coreutils`` so that
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37 ``readlink -e`` is supported across both Linux and MacOS
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38 platforms.
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39 0.38.0 - Update to Trimmomatic 0.38.
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40 0.36.6 - Added trimlog and log outputs; add support for
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41 ``fastqillumina`` and ``fastqsolexa`` input types
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42 0.36.5 - Remove tool_dependencies.xml and always use conda to resolve
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43 tool dependencies
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44 0.36.4 - Add option to provide custom adapter sequences for
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45 ILLUMINACLIP
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46 - Add options ``minAdapterLength`` and ``keepBothReads`` for
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47 ILLUMINACLIP in palindrome mode
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48 0.36.3 - Fix naming of output collections. Instead of all outputs being
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49 called "Trimmomatic on collection NN" these will now be called
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50 "Trimmomatic on collection NN: paired" or "Trimmomatic on
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51 collection NN: unpaired".
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52 0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as
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53 input the output will also be fastqsanger.gz.
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54 - Use $_JAVA_OPTIONS to customize memory requirements.
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55 0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed
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56 version is still supported for now).
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57 0.36.0 - Update to Trimmomatic 0.36.
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58 0.32.4 - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
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59 0.32.3 - Add support for FASTQ R1/R2 pairs using dataset collections
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60 (input can be dataset collection, in which case tool also
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61 outputs dataset collections) and improve order and naming of
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62 output files.
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63 0.32.2 - Use ``GALAXY_SLOTS`` to set the appropriate number of threads
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64 to use at runtime (default is 6).
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65 0.32.1 - Remove ``trimmomatic_adapters.loc.sample`` and hard-code
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66 adapter files into the XML wrapper.
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67 0.32.0 - Add tool_dependencies.xml to install Trimmomatic 0.32
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68 automatically and set the environment.
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69 - Update tool versioning to use Trimmomatic version number (i.e.
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70 ``0.32``) with tool iteration appended (i.e. ``.1``).
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71 0.0.4 - Specify '-threads 6' in <command> section.
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72 0.0.3 - Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of
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73 trimmomatic.
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74 0.0.2 - Updated ILLUMINACLIP option to use standard adapter sequences
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75 (requires the trimmomatic_adapters.loc file; sample version is
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76 supplied) plus cosmetic updates to wording and help text for
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77 some options.
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78 0.0.1 - Initial version
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79 ============== ================================================================
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82 Credits
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83 =======
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84
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85 This wrapper was originally developed and maintained by Peter Briggs
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86 (@pjbriggs).
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87 Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed
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88 support for gz compressed FastQ files. Charles Girardot (@cgirardot) and
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89 Jelle Scholtalbers (@scholtalbers) contributed additional options to
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90 ILLUMINACLIP.
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91 Matthias Bernt (@bernt-matthias) added log and trimlog output.
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d94aff5ee623 Version 0.38.1: add coreutils as dependency to fix tool issues with &#39;readlink -e&#39; across platforms.
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92 Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform
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93 support across Linux and MacOS.
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32f1f56bd970 Updated for Trimmomatic 0.39 and adds quality score options.
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94 Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39.
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95 Peter Briggs wishes to acknowledge the help from Matthia Bernt
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96 (@bernt-matthias) with relocating the tool in the IUC tool repository,
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97 and the IUC for taking on responsibility for the tool.
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99 Developers
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100 ==========
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101
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102 The Trimmomatic tool is now maintained as part of the ``tools-iuc`` repository
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103 on GitHub:
9a38087e3bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
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104 https://github.com/galaxyproject/tools-iuc/tools/tree/main/trimmomatic
1
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105
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106 Licence (MIT)
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107 =============
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108
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109 Permission is hereby granted, free of charge, to any person obtaining a copy
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110 of this software and associated documentation files (the "Software"), to deal
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111 in the Software without restriction, including without limitation the rights
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112 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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113 copies of the Software, and to permit persons to whom the Software is
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114 furnished to do so, subject to the following conditions:
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115
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116 The above copyright notice and this permission notice shall be included in
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117 all copies or substantial portions of the Software.
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118
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119 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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120 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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121 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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122 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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123 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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124 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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125 THE SOFTWARE.