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. ----- **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 ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/