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:

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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