A computer-based system for processing nucleotide sequence data, which are provided as reads, wherein the system has an interface for importing the nucleotide sequence data from a sequencer machine, the system further comprising: - A platform layer for holding process logic and an in-memory database system (IMDB) for processing nucleotide sequence data, wherein all processing steps for sequence alignment and variant calling, in particular for sort, merge, and indexing are directly executed in the in-memory database (IMDB), consisting of OLAP- and OLTP transactions; wherein the platform layer comprises: - a worker framework with a plurality of worker modules, wherein the worker modules are part of the in-memory database (IMDB) for executing data processing by means of data base operations and wherein each worker module is processing configurable and possible different alignment algorithms and is running on a computing node of a cluster and wherein the worker modules are processing in parallel and are adapted for providing partial alignment results (AR i) and wherein the worker modules are adapted for providing partial results of variant calling (VCR i), wherein all results and partial results are stored in the in-memory database (IMDB), - an updater framework for automatically downloading and importing annotation updates from external databases into the in-memory database (IMDB). - an alignment coordinator, which is adapted to provide the in-memory database (IMDB) with a modified alignment functionality, wherein the worker modules are adapted for alignment processing, so that at least one of a plurality of different alignment algorithms are integrated into the in-memory database, so that a specific alignment algorithm can be applied and wherein the alignment algorithms are adapted to be optimized for in-memory database use, and wherein the in-memory system (IMDB) is data storage for a web service, for all partial results of the method steps, for the nucleotide sequence to be aligned and for a reference sequence and wherein the system is based on a model view controller architecture pattern. - A platform layer for holding process logic and an in-memory database system (IMDB) for processing nucleotide sequence data, wherein all processing steps for sequence alignment and variant calling, in particular for sort, merge, and indexing are directly executed in the in-memory database (IMDB), consisting of OLAP- and OLTP transactions; wherein the platform layer comprises: - a worker framework with a plurality of worker modules, wherein the worker modules are part of the in-memory database (IMDB) for executing data processing by means of data base operations and wherein each worker module is processing configurable and possible different alignment algorithms and is running on a computing node of a cluster and wherein the worker modules are processing in parallel and are adapted for providing partial alignment results (AR i) and wherein the worker modules are adapted for providing partial results of variant calling (VCR i), wherein all results and partial results are stored in the in-memory database (IMDB), - an updater framework for automatically downloading and importing annotation updates from external databases into the in-memory database (IMDB). wherein all processing steps for sequence alignment and variant calling, in particular for sort, merge, and indexing are directly executed in the in-memory database (IMDB), consisting of OLAP- and OLTP transactions; wherein the platform layer comprises: - a worker framework with a plurality of worker modules, wherein the worker modules are part of the in-memory database (IMDB) for executing data processing by means of data base operations and wherein each worker module is processing configurable and possible different alignment algorithms and is running on a computing node of a cluster and wherein the worker modules are processing in parallel and are adapted for providing partial alignment results (AR i) and wherein the worker modules are adapted for providing partial results of variant calling (VCR i), wherein all results and partial results are stored in the in-memory database (IMDB), - an updater framework for automatically downloading and importing annotation updates from external databases into the in-memory database (IMDB). - a worker framework with a plurality of worker modules, wherein the worker modules are part of the in-memory database (IMDB) for executing data processing by means of data base operations and wherein each worker module is processing configurable and possible different alignment algorithms and is running on a computing node of a cluster and wherein the worker modules are processing in parallel and are adapted for providing partial alignment results (AR i) and wherein the worker modules are adapted for providing partial results of variant calling (VCR i), wherein all results and partial results are stored in the in-memory database (IMDB), - an updater framework for automatically downloading and importing annotation updates from external databases into the in-memory database (IMDB). - an alignment coordinator, which is adapted to provide the in-memory database (IMDB) with a modified alignment functionality, wherein the worker modules are adapted for alignment processing, so that at least one of a plurality of different alignment algorithms are integrated into the in-memory database, so that a specific alignment algorithm can be applied and wherein the alignment algorithms are adapted to be optimized for in-memory database use, and