Live Analysis of Pathogen NGS Data using Dynamic Compressible Indices

Next Generation Sequencing (NGS) has evolved as a main workhorse not only for molecular biology, but has also increasingly been used in clinical settings. For instance, unbiased, open-view pathogen diagnostics or personalized medicine applications heavily depend on the large-scale resolution of NGS analyses. At the same time, these applications require fast turnaround time of analyses and have high computational demands due to comparisons to very large databases that show exponential increase in size.

The standard paradigm of NGS analysis focuses on a sequential setup where sequencers are first run, data is transferred to computing servers afterwards, and then analyzed. Analysis is usually carried out by comparison of all reads against a single index with pre-defined and constant parameters for all reads. Numerous tools exist including e.g. BWA or Yara and RazerS3, which were built using our SeqAn library that is supported within the Center of Integrative Bioinformatics (CIBI) as part of the German Network for Bioinformatics Infrastructure (de.NBI). While powerful in many molecular biology settings, this paradigm has major limitations for time-critical diagnostic applications that we aim to overcome within this project.

The project started on 1 April 2019 and terminated on 30 June 2022.