NanoPack: visualizing and processing long-read sequencing data

NanoPack: visualizing and processing long-read sequencing data

2018 | Wouter De Coster, Svenn D'Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
NanoPack is a set of Python scripts designed for visualizing and processing long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. These tools, developed by researchers from the Neurodegenerative Brain Diseases Group at VIB & University of Antwerp and the Department of Biomolecular Engineering and Bioinformatics at the University of California Santa Cruz, aim to address the limitations of existing QC tools tailored for short-read sequencing data. NanoPack includes scripts for statistical evaluation and visualization (NanoStar, NanoPlot, NanoComp) and data processing (NanoFilt, NanoLyse). The software is available under the GNU GPL3.0 License and can be installed via PyPI and bioconda. It supports various input formats and provides flexible plotting options, including bivariate plots and log-scale read length plots. Examples and detailed documentation are provided, demonstrating the effectiveness of NanoPack in analyzing long-read sequencing data, such as an ONT Escherichia coli dataset. The package is accessible through a graphical user interface, web service, and command-line tools, making it a comprehensive solution for long-read sequencing data analysis.NanoPack is a set of Python scripts designed for visualizing and processing long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. These tools, developed by researchers from the Neurodegenerative Brain Diseases Group at VIB & University of Antwerp and the Department of Biomolecular Engineering and Bioinformatics at the University of California Santa Cruz, aim to address the limitations of existing QC tools tailored for short-read sequencing data. NanoPack includes scripts for statistical evaluation and visualization (NanoStar, NanoPlot, NanoComp) and data processing (NanoFilt, NanoLyse). The software is available under the GNU GPL3.0 License and can be installed via PyPI and bioconda. It supports various input formats and provides flexible plotting options, including bivariate plots and log-scale read length plots. Examples and detailed documentation are provided, demonstrating the effectiveness of NanoPack in analyzing long-read sequencing data, such as an ONT Escherichia coli dataset. The package is accessible through a graphical user interface, web service, and command-line tools, making it a comprehensive solution for long-read sequencing data analysis.
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