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---
name: Trimmomatic
url: http://www.usadellab.org/cms/?page=trimmomatic
description: >
Trimmomatic is a flexible read trimming tool for Illumina NGS data
---
The Trimmomatic module parses standard error generated by
[Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic),
a flexible read trimming tool for Illumina NGS data. StdErr can be captured by
directing it to a file e.g. `trimmomatic command 2> trim_out.log`
By default, the module generates the sample names based on the input FastQ file names in
the command line used by Trimmomatic. If you prefer, you can tell the module to use
the filenames as sample names instead. To do so, use the following config option:
```yaml
trimmomatic:
s_name_filenames: true
```
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