Comparing runs of Oxford Nanopore sequencing data and alignments
Project description
Compare multiple runs of Oxford Nanopore sequencing data and alignments
INSTALLATION
pip install NanoComp
This script is written for Python3.
USAGE
NanoComp [-h] [-v] [-t THREADS] [--readtype {1D,2D,1D2}] [-o OUTDIR]
[-p PREFIX]
[-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
[-n [NAMES [NAMES ...]]]
(--fastq [FASTQ [FASTQ ...]] | --summary [SUMMARY [SUMMARY ...]] | --bam [BAM [BAM ...]])
optional arguments:
-h, --help show this help message and exit
-v, --version Print version and exit.
-t, --threads THREADS Set the allowed number of threads to be used by the script
--readtype {1D,2D,1D2}
Which read type to extract information about from
summary. Options are 1D, 2D, 1D2
-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.
-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 [NAMES ...]]
Specify the names to be used for the datasets
--plot {violin,box} Which plot type to use: boxplot or violinplot (default)
--fastq [FASTQ [FASTQ ...]]
Data is in default fastq format.
--summary [SUMMARY [SUMMARY ...]]
Data is a summary file generated by albacore.
--bam [BAM [BAM ...]]
Data as a sorted bam file.
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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