We develop novel tools and workflows for handling large amounts of sequence data. We apply computational methods to automate de novo (meta-)genome and transcriptome assembly, analysis and annotation of RNA-Seq data, identification and characterization of pathogens such as viruses and bacteria from environmental samples and (more recently) molecular monitoring of infectious diseases.
We strive to combine well-established and novel computational approaches into reproducible workflows to analyze and visualize large amounts of short- and long-read sequencing data.
Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done! In the latest preprint, we investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data.08. May 2021
Many laboratories have ramped up nanopore sequencing for SARS-CoV-2 surveillance, but are in dire need of bioinformatics support. Here we present poreCov, a high-throughput software pipeline for reliable genotyping and reference-based genome reconstruction of SARS-CoV-2 samples based on nanopore tiled amplicon sequencing focused around the ARTIC protocol. On GitHub! Big kudos @CaSe Group Jena!11. April 2021
Our chromosome-level hybrid genome assembly with RNA-Seq-improved annotation of the oleaginous yeast Rhodotorula toruloides is out as a preprint! Great collaboration w/ the Swedish University of Agricultural Sciences, Uppsala (SLU)!