Read Aligner API


Read Aligner API



Advancements in DNA read alignment algorithms have resulted in a number of read alignment tools that have different qualities and different APIs. Evaluating the various tools in the same pipeline can be challenging because of their incompatible interfaces. Moreover, these tools generally don’t provide an easy-to-use programming interface to allow their seamless integration into novel software or workflows.


RAPI defines a C API for a short read aligner (to map short reads to a reference sequence) and high-level Python and Java interfaces. It also includes a reference implementation that wraps BWA-MEM and Python bindings for the API. RAPI can be used to integrate new read alignment software in existing RAPI-compliant software. It can also be used to allow simple Python scripting with standard read alignment algorithms or integration in JVM environments (Java, Scala, etc.).

Innovative features

  • standard multi-aligner API;
  • high-level, high-performance Python interface.

Potential users

Bioinformaticians, researchers, sequencing centers professionals.

Impact sectors

Health - Biomedicine - ICT

Other resources

  2. L.Pireddu, S. Leo, G. Zanetti; SEAL: a distributed short read mapping and duplicate removal tool, Bioinformatics, Volume 27, Issue 15, 1 August 2011, Pages 2159–2160,

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