MAIRA - Highly efficient and accurate algorithms for mobile analysis of microbes

• Applicant: Professor Dr. Daniel H. Huson
• Subject Area: Bioinformatics and Theoretical Biology ; Parasitology and Biology of Tropical Infectious Disease Pathogens
• Term: from 2015 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 289436404

Bioinformatics is a technology-driven research area and a new exciting technological development is mobile sequencing. This is based on the Oxford Nanopore MinION. This is a small USB device that performs single molecule sequencing. Mobile sequencing will open many new research opportunities by greatly reducing the time from sample collection to completed sequencing, and by allowing sequencing to be taken into the field. The aim of this project is to develop a suite of new algorithms that perform highly efficient and accurate mobile analysis of microbes. The algorithms will analyze sequences as soon as their first bases start coming of the mobile sequencer in an online fashion, giving early feedback on the microbial content of a sample. The algorithms will seek to identify microbes down to the strain-level by performing a careful analysis of the detected gene content. A key problem is to perform a fast alignment of reads against a large database of known microbes. This will be addressed using state-of-the-art algorithmic techniques such as so-called double indexing and spaced seeds. Strain-level identification is a difficult problem and new algorithms will be developed to address this. The new algorithms will be made available in a computer program called MAIRA, an acronym for microbe identification using rapid algorithms.

• DFG Programme: Research Grants