A computer-based system for the alignment of genomic sequence data, which are provided as reads, wherein the system has an interface for importing the genomic sequence data from a sequencer machine, wherein the system comprises: - a platform layer for holding process logic and an in-memory database system (IMDB) for processing genomic sequence data, wherein all processing steps and tools for sequence alignment and variant calling and in particular for sort, merge and indexing are directly executed by the in-memory database system (IMDB), consisting of OLAP- and OLTP transactions; wherein the platform layer comprises: - a worker framework with a plurality of workers, - wherein each worker is processing configurable alignment algorithms and is running on a computing node of a cluster with multiple CPU cores and - wherein the workers are processing in parallel and wherein an index data structure, being a single or two-array index data structure, is computed and stored in the in-memory database (IMDB) and replicated over local memory of processor sockets or over multiple computing nodes of the cluster in order to allow for on-the-fly read alignments on a massive parallel machine and - wherein all results and intermediate results are stored in the in-memory database (IMDB), and - an updater framework for automatically downloading and importing annotation updates from a selection of external databases into the in-memory database (IMDB), - an alignment coordinator, which is adapted to provide the in-memory database system (IMDB) with a modified alignment functionality, which allows applying different alignment algorithms, being integrated into the in-memory database (IMDB). - a platform layer for holding process logic and an in-memory database system (IMDB) for processing genomic sequence data, wherein all processing steps and tools for sequence alignment and variant calling and in particular for sort, merge and indexing are directly executed by the in-memory database system (IMDB), consisting of OLAP- and OLTP transactions; wherein the platform layer comprises: - a worker framework with a plurality of workers, - wherein each worker is processing configurable alignment algorithms and is running on a computing node of a cluster with multiple CPU cores and - wherein the workers are processing in parallel and wherein an index data structure, being a single or two-array index data structure, is computed and stored in the in-memory database (IMDB) and replicated over local memory of processor sockets or over multiple computing nodes of the cluster in order to allow for on-the-fly read alignments on a massive parallel machine and - wherein all results and intermediate results are stored in the in-memory database (IMDB), and - an updater framework for automatically downloading and importing annotation updates from a selection of external databases into the in-memory database (IMDB), - a worker framework with a plurality of workers, - wherein each worker is processing configurable alignment algorithms and is running on a computing node of a cluster with multiple CPU cores and - wherein the workers are processing in parallel and wherein an index data structure, being a single or two-array index data structure, is computed and stored in the in-memory database (IMDB) and replicated over local memory of processor sockets or over multiple computing nodes of the cluster in order to allow for on-the-fly read alignments on a massive parallel machine and - wherein all results and intermediate results are stored in the in-memory database (IMDB), and - wherein each worker is processing configurable alignment algorithms and is running on a computing node of a cluster with multiple CPU cores and - wherein the workers are processing in parallel and wherein an index data structure, being a single or two-array index data structure, is computed and stored in the in-memory database (IMDB) and replicated over local memory of processor sockets or over multiple computing nodes of the cluster in order to allow for on-the-fly read alignments on a massive parallel machine and - wherein all results and intermediate results are stored in the in-memory database (IMDB), and - an updater framework for automatically downloading and importing annotation updates from a selection of external databases into the in-memory database (IMDB), - an alignment coordinator, which is adapted to provide the in-memory database system (IMDB) with a modified alignment functionality, which allows applying different alignment algorithms, being integrated into the in-memory database (IMDB).