MA – The Modular Aligner (Installer Download)

LogoMA is a flexible high-throughput aligner suitable for long and short reads of various sequencing techniques (Illumina, Pacific Biosciences, Oxford Nanopore Technologies). It has a modular design and relies on a transparent algorithmic frame for achieving high accuracy in combination with high throughput. MA is available via GitHub:


  • Performant and highly accurate
  • For long read as well as short reads
  • Usable via command line or convenient graphical user interface
  • Extensive Python support on module level without computational penalty. (A precompiled pyd-file comes with the installer.)
  • Installer for Microsoft Windows Windows® (64 bit)
For Microsoft Windows Windows® (64 bit, Windows 7 or Windows 10), you can get an installer for MA via the download button below:

Important Remark:
The MA-installer is not digitally signed. Therefore, after starting the installer, Windows Defender might complain about an “Unrecognized app” and might suggest that continuing the installation could put your PC on risk due to an “Unknown publisher”. In order to continue, please click on “More Info” and then on the button “Run anyway”. We would like to apologize for this inconvenience during installation.

Hardware requirements

8GB of memory is the recommended minimum for aligning reads with respect to the human genome. For large scale high-throughput alignments, a multi-core processor with at least 4 cores is preferable. In the case of processors with 16 cores or more, we advise the use of a SSD for SAM-output. Otherwise, bandwidth limitations of the output medium can hurt the overall performance.

Python support

If MA is compiled with Python support, the resulting binaries contain a file “libMA.pyd” that comprises a Python module for aligner construction and prototyping via Python scripts. The GitHub page of MA contains an example of such an aligner in the folder “python/MA”.

More Info

On the GitHub page:

Arne Kutzner, Markus Schmidt (2019)

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