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

Runs under Python 3.6 to 3.9 (though 7 of 1682 tests fail under 3.7 due to the unittest module and mocking of open). Change log

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.

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

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

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.

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.

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

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

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

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