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NGI Visualizations

A collection of next-gen sequencing visualisation scripts. Click a script's name to go to it's subdirectory which will contain a detailed README.md file with examples and instructions.


Depreciation notice

Please Note that many of these scripts have been superseded by MultiQC (http://multiqc.info). if you're not familiar with it we recommend having a look there first before using the tools below.


Introduction

Most of these scripts are written in Python. Those within the stand_alone are generally run on the command line. The rest can either be run on the command line or imported as part of the ngi_visualizations package. See below for instructions on how to use the python package.

Examples

See below for example outputs. Click an image to go to that script.

Count Biotypes
preseq Complexity Curves Subsampled Gene Observations
Qualimap Plots
snpEff Effect Plots
Gene Body Coverage FPKM Scatter Plot
Alignment Summaries Bismark Summaries
Bismark Coverage Curves Bismark Window Sizes

Usage

For using stand alone packages see the README.md file in that package's subdirectory.

To use the ngi_visulaizations package, download or clone the repository. Then, to install the package, run:

python setup.py install

If you intend to make any changes to the package, swap install for develop, else you will have to reinstall the package each time you change the source code.

Once installed, you can import the script from the relevant subdirectory. For instance, to use the Qualimap Insert Size histogram you would use:

from ngi_visulaizations.qualimap import insert_size

The functions within this script are then available in that namespace. For instance, you could now generate the histograms by running:

insert_size.plot_insert_size_histogram(input_fn)

Contributing

If you would like to add a visualization script to this repository, please read the contributing notes first. These describe the steps required in adding your script to the repository.

Credits

These scripts were written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden. For more information, please get in touch with Phil Ewels.

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Next-Gen Sequencing Visualisation Scripts.

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