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Create fastQC-like plots for Oxford Nanopore sequencing data

Project description

nanoQC

Quality control tools for long read sequencing data aiming to replicate some of the plots made by fastQC. This is an immature tool and I welcome all contributions.

Twitter URL install with conda

Creates dynamic plots using bokeh. For an example see here

INSTALLATION

pip install nanoQC

or
install with conda

conda install -c bioconda nanoqc

USAGE

nanoQC [-h] [-v] [-o OUTDIR] fastq

positional arguments:
  fastq                 Reads data in fastq.gz format.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Print version and exit.
  -o, --outdir OUTDIR   Specify directory in which output has to be created.
  -l, --minlen int      Minimum length of reads to be included in the plots
                        This also controls the length plotted in the graphs
                        from the beginning and end of reads (length plotted = minlen / 2)

CITATION

If you use this tool, please consider citing our publication.

CONTRIBUTIONS

Thanks to:

  • Jasper Ouwerkerk (JasperO98) for improving how reads are selected (v0.8.0)

Project details


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Files for nanoQC, version 0.9.2
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