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        "author": "Marcus Stoiber",
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        "description": "Summary\r\n-------\r\n\r\nThis package provides tools for the analysis of raw nanopore sequencing\r\ndata, including correction of basecalls and visualization.\r\n\r\nFull Documentation\r\n------------------\r\n\r\nFull documentation avaialable at Read the Docs: https://nanoraw.readthedocs.io\r\n\r\nInstallation\r\n------------\r\n\r\nInstall nanoraw without plotting dependencies (base genome_resquiggle algorithm and text outputs: wig and fasta)\r\n\r\n::\r\n\r\n   pip install nanoraw\r\n\r\nInstall nanoraw with plotting dependencies (requires separate installation of R packages ggplot2 and cowplot)\r\n\r\n::\r\n\r\n   pip install nanoraw[plot]\r\n\r\nInstall nanoraw via pip\r\n\r\n::\r\n\r\n    pip install nanoraw\r\n\r\nInstall bleeding edge via github\r\n\r\n::\r\n\r\n    pip install git+https://github.com/marcus1487/nanoraw.git\r\n\r\nUsage\r\n-----\r\n\r\n::\r\n\r\n    nanoraw -h\r\n    nanoraw [command] [options]\r\n\r\n\r\nMain Command (Must be run before any other commands):\r\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n\r\n-   :code:`genome_resquiggle`: Re-annotate raw signal with genomic aignement of existing basecalls.\r\n\r\nGenome Anchored Plotting Commands:\r\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n\r\n-   :code:`plot_max_coverage`: Plot signal in regions with the maximum coverage.\r\n-   :code:`plot_genome_location`: Plot signal at defined genomic locations.\r\n-   :code:`plot_motif_centered`: Plot signal at regions centered on a specific motif.\r\n-   :code:`plot_max_difference`: Plot signal where signal differs the most between two groups.\r\n-   :code:`plot_most_significant`: Plot signal where signal differs the most significantly between two groups.\r\n-   :code:`plot_motif_with_stats`: Plot signal from several regions and test statistics centered on a motif of interst.\r\n\r\nSequencing Time Anchored Plotting Command:\r\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n\r\n-   :code:`plot_correction`: Plot segmentation before and after correction.\r\n-   :code:`plot_multi_correction`: Plot multiple raw signals anchored by genomic location.\r\n\r\nOther Plotting Command:\r\n^^^^^^^^^^^^^^^^^^^^^^^\r\n\r\n-   :code:`plot_kmer`: Plot signal quantiles acorss kmers.\r\n-   :code:`cluster_most_significant`: Clustering traces at bases with significant differences.\r\n\r\nAuxiliary Command:\r\n^^^^^^^^^^^^^^^^^^\r\n\r\n-  :code:`write_most_significant_fasta`: Write sequence where signal differs the most significantly between two groups.\r\n-  :code:`write_wiggles` :  Write wiggle files for nanopore signal values, coverage, and statistics.\r\n\r\n    Get additional help for subcommands with ``nanoraw [command] -h``\r\n\r\nRequirements\r\n------------\r\n\r\n-  HDF5 (http://micro.stanford.edu/wiki/Install_HDF5#Install)\r\n-  graphmap (https://github.com/isovic/graphmap)\r\n   OR\r\n-  BWA-MEM (<http://bio-bwa.sourceforge.net/>)\r\n\r\npython Requirements:\r\n^^^^^^^^^^^^^^^^^^^^\r\n\r\n-  numpy\r\n-  scipy\r\n-  h5py\r\n\r\nOptional plotting packages (install R packages with `install.packages([package_name])` from an R prompt):\r\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\r\n\r\n-  rpy2 (python package; with R installation)\r\n-  ggplot2 (required for all plotting subcommands)\r\n-  cowplot (required for plot_motif_with_stats subcommand)\r\n\r\nCitation\r\n--------\r\n\r\nStoiber, M.H. et al. De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. bioRxiv (2016).\r\n\r\nhttp://biorxiv.org/content/early/2017/04/10/094672\r\n\r\nLegal\r\n-----\r\n\r\nnanoraw v.1 Copyright (c) 2016, The Regents of the University of\r\nCalifornia, through Lawrence Berkeley National Laboratory (subject to\r\nreceipt of any required approvals from the U.S. Dept. of Energy). All\r\nrights reserved.\r\n\r\nIf you have questions about your rights to use or distribute this\r\nsoftware, please contact Berkeley Lab's Innovation and Partnerships\r\ndepartment at IPO@lbl.gov referring to \" nanoraw v.1 (2016-199).\"\r\n\r\nNOTICE. This software was developed under funding from the U.S.\r\nDepartment of Energy. As such, the U.S. Government has been granted for\r\nitself and others acting on its behalf a paid-up, nonexclusive,\r\nirrevocable, worldwide license in the Software to reproduce, prepare\r\nderivative works, and perform publicly and display publicly. Beginning\r\nfive (5) years after the date permission to assert copyright is obtained\r\nfrom the U.S. Department of Energy, and subject to any subsequent five\r\n(5) year renewals, the U.S. Government is granted for itself and others\r\nacting on its behalf a paid-up, nonexclusive, irrevocable, worldwide\r\nlicense in the Software to reproduce, prepare derivative works,\r\ndistribute copies to the public, perform publicly and display publicly,\r\nand to permit others to do so.",
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