dark-matter 7.1.13

Python library and utility scripts for working with genetic sequence data.

Dark matter

A collection of Python tools for filtering and visualizing Next Generation Sequencing reads.

Installation

On Linux (at least) you will need to first:

sudo apt install zlib1g-dev libbz2-dev liblzma-dev

Then you should be able to install via

$ pip install dark-matter

Some additional information is available for Linux, OS X, and Windows.

Optional dependencies

Not all of the following are mandatory. It depends which part of the dark-matter code you try to use.

Picard

run-bowtie2.py can use Picard to mark duplicates.

GATK

run-bowtie2.py uses gatk if you call it with --markDuplicatesGATK or --callHaplotypesGATK. If you want to do this you'll need to download the gatk zip file, unzip it, and either put the directory where you unzip it into your shell's path or else move the contents of the zip file into a directory already in your path.

bcftools

You'll need bcftools if you want to make consensuses using the make-consensus.py script. Either follow the installation instructions or, if you use brew (or Linux brew), brew install bcftools.

samtools

The run-bowtie2.py and run-bwa.py scripts both make use of samtools.

EMBOSS

The compare-sequences.py script (if called with --align) requires the needle and (possibly) stretcher from EMBOSS.

iPython Notebook

If you are using dark matter in an iPython Notebook, you should install the requirements in requirements-ipynb.txt.

Development

If you are using dark matter as a developer, you should install the requirements in requirements-dev.txt.