Welcome

We are a bioinformatics team at the FSU Jena focusing on transcriptomics and metagenomics using short and long reads.

We develope tools and workflows to handle large sequencing data sets. We apply our computational methods to de novo genome and transcriptome assembly, the comprehensive analysis of RNA-Seq data, and the identification and characterization of pathogens such as viruses and bacteria from environmental samples.

We strive to combine well-established and novel computational approaches to analyze and visualize large amounts of short- and long-read sequencing data.

We work closely with the RNA Bioinformatics/High-Throughput group of Manja Marz and we are a member of the European Virus Bioinformatics Center.


Research Interests

  • Bioinformatics
  • Transcriptomics & comparative genomics
  • de novo assembly & annotation
  • Microbes & viruses
  • Metagenomics & -transcriptomics
  • Oxford Nanopore Sequencing
  • Non-coding RNA & RNA secondary structure
  • Automation & visualization

ONT hybrid MAGs







News

10. February 2020

Are you looking for some easy to run tool w/o dependency-struggle to analyze your hybrid metagenomics data? Including state-of-the-art principals of diff binning and pathways? Check out MUFFIN!

02. February 2020

Our pipeline RIBAP for the automatic annotation and core gene set calculation/visualization of bacterial genomes is now available as a Nextflow/Docker/Conda workflow. Annotate your protein sequences with Prokka and determine a pan genome with Roary. This genome is refined with the usage of ILPs that solve the best matching for each pairwise strain mmseqs2 comparison.

06. January 2020

Already in the old year Lasse submitted his master's thesis, which dealt with the efficient clustering of multi-tool transcriptome assemblies. Now he is about to take his bioinformatics knowledge out into the world. We wish him all the best and much success for his future career!

... see all News