fastx_toolkit
fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output
**What it does**
Creates a boxplot graph for the quality scores in the library.
.. class:: infomark
**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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**Output Examples**
* Black horizontal lines are medians
* Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
* Whiskers show outlier at max. 1.5*IQR
An excellent quality library (median quality is 40 for almost all 36 cycles):
.. image:: ../static/fastx_icons/fastq_quality_boxplot_1.png
A relatively good quality library (median quality degrades towards later cycles):
.. image:: ../static/fastx_icons/fastq_quality_boxplot_2.png
A low quality library (median drops quickly):
.. image:: ../static/fastx_icons/fastq_quality_boxplot_3.png
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This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
.. __: http://hannonlab.cshl.edu/fastx_toolkit/