NanoPlot

NanoPlot is a tool for plotting long read sequencing data and alignments. It generates a statistical summary, various plots, and an HTML summary file.

Basic Usage Patterns:

• From a summary file (fastest):

  NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed

• From FASTQ files with filtering and specific plot types:

  NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots dot --legacy hex

• From BAM files with downsampling:

  NanoPlot --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled

NanoPlot can be installed using pip or conda. It is written for Python 3.

Using pip:

pip install NanoPlot

To upgrade to a newer version:

pip install NanoPlot --upgrade

Using conda:

conda install -c bioconda nanoplot

Use these options to modify the data before plotting:

General flags for controlling execution and output directory:

NanoPlot requires exactly one of the following input source flags. You can provide multiple files for most of these.