Comparing runs of Oxford Nanopore sequencing data and alignments
Project description
Compare multiple runs of long read sequencing data and alignments
INSTALLATION
pip install NanoComp
This script is written for Python3.
USAGE
NanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose] [--raw] [--readtype {1D,2D,1D2}] [--barcoded] [--split_runs TSV_FILE] [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}] [-n names [names ...]] [--plot {violin,box}] [--title TITLE] (--fastq files [files ...] | --summary files [files ...] | --bam files [files ...]) General options: -h, --help show the help and exit -v, --version Print version and exit. -t, --threads THREADS Set the allowed number of threads to be used by the script -o, --outdir OUTDIR Specify directory in which output has to be created. -p, --prefix PREFIX Specify an optional prefix to be used for the output files. --verbose Write log messages also to terminal. --raw Store the extracted data in tab separated file. Options for filtering or transforming input prior to plotting: --readtype {1D,2D,1D2} Which read type to extract information about from summary. Options are 1D, 2D, 1D2 --barcoded Barcoded experiment in summary format, splitting per barcode. --split_runs TSV_FILE File: Split the summary on run IDs and use names in tsv file. Mandatory header fields are 'NAME' and 'RUN_ID'. Options for customizing the plots created: -f, --format {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff} Specify the output format of the plots. -n, --names names Specify the names to be used for the datasets -c, --colors colors Specify the colors to be used for the datasets --plot {violin,box} Which plot type to use: boxplot or violinplot (default) --title TITLE Add a title to all plots, requires quoting if using spaces Input data sources, one of these is required.: --fastq files [files ...] Data is in (compressed) fastq format. --fasta files [files ...] Data is in (compressed) fasta format. --summary files [files ...] Data is in (compressed) summary files generated by albacore. --bam files [files ...] Data is in sorted bam files.
EXAMPLES
NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4
EXAMPLE OUTPUT
I welcome all suggestions, bug reports, feature requests and contributions. Please leave an issue or open a pull request. I will usually respond within a day, or rarely within a few days.
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