This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
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Project Description

Summary

This package provides tools for the analysis of raw nanopore sequencing data, including correction of basecalls and visualization.

Installation

Install nanoraw via pip

pip install nanoraw

Install bleeding edge via github

pip install git+https://github.com/marcus1487/nanoraw.git

Usage

nanoraw -h
nanoraw [command] [options]

Main Comand (Must be run before any other commands):

  • genome_resquiggle: Re-annotate raw signal with genomic aignement of existing basecalls.

Genome Anchored Plotting Commands:

  • plot_max_coverage: Plot signal in regions with the maximum coverage.
  • plot_genome_location: Plot signal at defined genomic locations.
  • plot_kmer_centered: Plot signal at regions centered on a specific kmer.
  • plot_max_difference: Plot signal where signal differs the most between two groups.
  • plot_most_significant: Plot signal where signal differs the most significantly between two groups.
  • plot_kmer_with_stats: Plot signal from several regions and test statistics centered on a k-mer of interst.

Sequencing Time Anchored Plotting Command:

  • plot_correction: Plot segmentation before and after correction.
  • plot_multi_correction: Plot multiple raw signals anchored by genomic location.

Other Plotting Command:

  • plot_kmer: Plot signal quantiles acorss kmers.
  • cluster_most_significant: Clustering traces at bases with significant differences.

Auxiliary Command:

  • write_most_significant: Write sequence where signal differs the most significantly between two groups.

  • write_wiggle : Write wiggle file of genome coverage from genome_resquiggle mappings.

    Get additional help for subcommands with nanoraw [command] -h

Requirements

python Requirements:

  • numpy
  • scipy
  • h5py
  • rpy2

Optional python Package:

  • Biopython (for robust FASTA parsing, but a simple parser is provided)

Optional R Packages (install with install.packages([package_name]) from an R prompt):

  • changepoint (for using R’s changepoint package for re-segmentation)
  • ggplot2 (required for all plotting subcommands)
  • cowplot (required for plot_kmer_with_stats subcommand)
Release History

Release History

0.3

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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0.2

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TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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0.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
nanoraw-0.3.tar.gz (37.2 kB) Copy SHA256 Checksum SHA256 Source Nov 28, 2016

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