fastx_toolkit fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output **What it does** Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. .. class:: infomark **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool. ----- **Output Examples** The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png But most of the time, the chart will look rather random: .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/