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Comparing runs of Oxford Nanopore sequencing data and alignments

Project description

Compare multiple runs of long read sequencing data and alignments

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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 default fastq format.
  --summary files [files ...]
                        Data is a summary file generated by albacore.
  --bam files [files ...]
                        Data as a sorted bam file.

Example file for –split_runs

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

loglength example box percentIdentity example

See more examples

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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