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
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 [NAMES [NAMES ...]]
Specify the names to be used for the datasets
--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.
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NanoComp-0.3.1.tar.gz
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