Plotting suite for Oxford Nanopore sequencing data and alignments
Project description
Plotting tool for Oxford Nanopore sequencing data and alignments.
In addition to various plots also a NanoStats file is created
summarizing key features of the dataset.
Example plot
The example plot above shows a bivariate plot comparing log transformed read length with average basecall Phred quality score. More examples can be found in the gallery on my blog ‘Gigabase Or Gigabyte’.
This script performs data extraction from Oxford Nanopore sequencing
data in the following formats:
- fastq files
(can be bgzip, bzip2 or gzip compressed)
- fastq files generated by albacore or MinKNOW containing additional
information
(can be bgzip, bzip2 or gzip compressed)
- sorted bam files
- sequencing_summary.txt output table generated by albacore
Installation
pip install NanoPlot
Upgrade to a newer version using:
pip install NanoPlot --upgrade
The script is written for python3 but also seems to work for python2.7.
USAGE:
NanoPlot [-h] [-v] [-t THREADS] [--maxlength MAXLENGTH] [--drop_outliers] [--downsample DOWNSAMPLE] [--loglength] [--alength] [-o OUTDIR] [-p PREFIX] (--fastq FASTQ | --fastq_rich FASTQ_RICH | --summary SUMMARY | --bam BAM) Required input argument is (exact) one of these: --fastq FASTQ Data presented is in fastq format exported from fast5 files by e.g. poretools. --fastq_rich FASTQ_rich Data presented is in fastq format generated by Albacore or MinKNOW with additional information concerning channel and time. --bam BAM Data presented as a sorted bam file. --summary SUMMARY Data is a summary file generated by albacore. Each of these options can take one or multiple files e.g. --summary summary1.txt summary2.txt summary3.txt --bam bam1.txt bam2.txt Arguments for optional filtering: --readtype Specify read type to extract from summary file Options: 1D (default), 2D --maxlength MAXLENGTH Drop reads longer than length N. --downsample DOWNSAMPLE Reduce dataset to N reads by random sampling. --drop_outliers Drop outlier reads with extreme long length. --loglength Logarithmic scaling of lengths in plots. --alength Use aligned read lengths rather than sequenced length (bam mode). Optional output arguments: -o, --outdir OUTDIR Specify directory in which output has to be created. -p, --prefix PREFIX Specify a prefix to be used for the output files. -c, --color COLOR Specify a color for the plots must be a valid matplotlib color (see color_options.txt) default: green -f, --format FORMAT Specify the output format for the plots, options are: eps, jpg, pdf, png, ps, svg default: png --plots PLOTS Specify which type of bivariate plots have to be made options are: hex, kde, dot (multiple can be specified together) default: all General arguments: -h, --help show this help message and exit -v, --version Print version and exit. -t, --threads THREADS Max number of threads to be used by the script
Companion scripts
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NanoPlot-0.16.1.tar.gz
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