Repository README files - may contain important installation or license information

Trimmomatic: flexible read trimming tool for Illumina NGS data

Galaxy tool wrapper for the Trimmomatic program, which provides various functions for manipluating Illumina FASTQ files (both single and paired-end).

Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university http://www.usadellab.org/cms/index.php?page=trimmomatic

The reference for Trimmomatic is:

Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.

Controlling the available memory

The default amount of memory avilable to trimmomatic is set to 8GB. To change the default amount of memory you can set the environment variable _JAVA_OPTIONS to -Xmx<amount_of_memory_in_GB>G. The recommended way to set this is in the job_conf.xml file. To change the available memory to 6GB, a line like the below should be added:

<env id="_JAVA_OPTIONS">-Xmx6G</env>

This will set the environment variable _JAVA_OPTIONS to -Xmx6G.

History

Version	Changes
0.39+galaxy1	Relocated to the `tools-iuc` repository
0.39	Update to Trimmomatic 0.39.
0.38.1	Bug fix: add dependency on `coreutils` so that `readlink -e` is supported across both Linux and MacOS platforms.
0.38.0	Update to Trimmomatic 0.38.
0.36.6	Added trimlog and log outputs; add support for `fastqillumina` and `fastqsolexa` input types
0.36.5	Remove tool_dependencies.xml and always use conda to resolve tool dependencies
0.36.4	Add option to provide custom adapter sequences for ILLUMINACLIP Add options `minAdapterLength` and `keepBothReads` for ILLUMINACLIP in palindrome mode
0.36.3	Fix naming of output collections. Instead of all outputs being called "Trimmomatic on collection NN" these will now be called "Trimmomatic on collection NN: paired" or "Trimmomatic on collection NN: unpaired".
0.36.2	Support fastqsanger.gz datatype. If fastqsanger.gz is used as input the output will also be fastqsanger.gz. Use $_JAVA_OPTIONS to customize memory requirements.
0.36.1	Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
0.36.0	Update to Trimmomatic 0.36.
0.32.4	Add support for `AVGQUAL` and `MAXINFO` operations.
0.32.3	Add support for FASTQ R1/R2 pairs using dataset collections (input can be dataset collection, in which case tool also outputs dataset collections) and improve order and naming of output files.
0.32.2	Use `GALAXY_SLOTS` to set the appropriate number of threads to use at runtime (default is 6).
0.32.1	Remove `trimmomatic_adapters.loc.sample` and hard-code adapter files into the XML wrapper.
0.32.0	Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and set the environment. Update tool versioning to use Trimmomatic version number (i.e. `0.32`) with tool iteration appended (i.e. `.1`).
0.0.4	Specify '-threads 6' in <command> section.
0.0.3	Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic.
0.0.2	Updated ILLUMINACLIP option to use standard adapter sequences (requires the trimmomatic_adapters.loc file; sample version is supplied) plus cosmetic updates to wording and help text for some options.
0.0.1	Initial version

Credits

This wrapper was originally developed and maintained by Peter Briggs (@pjbriggs). Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed support for gz compressed FastQ files. Charles Girardot (@cgirardot) and Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. Matthias Bernt (@bernt-matthias) added log and trimlog output. Nicola Soranzo (@nsoranzo) suggested using coreutils to enable cross-platform support across Linux and MacOS. Cristóbal Gallardo (@gallardoalba) updated Trimmomatic up to version 0.39. Peter Briggs wishes to acknowledge the help from Matthia Bernt (@bernt-matthias) with relocating the tool in the IUC tool repository, and the IUC for taking on responsibility for the tool.

Developers

The Trimmomatic tool is now maintained as part of the tools-iuc repository on GitHub: https://github.com/galaxyproject/tools-iuc/tools/tree/main/trimmomatic

Licence (MIT)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.