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Book Chapter

MAIRA: Protein-based Analysis of MinION Reads on a Laptop


Bağci,  C       
IMPRS From Molecules to Organisms, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Bağci, C., Abrecht, B., & Huson, D. (2023). MAIRA: Protein-based Analysis of MinION Reads on a Laptop. In S. Mitra (Ed.), Metagenomic Data Analysis (pp. 223-234). NewYork, NY, USA: Humana Press.

Cite as: https://hdl.handle.net/21.11116/0000-000D-3A54-4
Third-generation sequencing technologies are being increasingly used in microbiome research and this has given rise to new challenges in computational microbiome analysis. Oxford Nanopore's MinION is a portable sequencer that streams data that can be basecalled on-the-fly. Here we give an introduction to the MAIRA software, which is designed to analyze MinION sequencing reads from a microbiome sample, as they are produced in real-time, on a laptop. The software processes reads in batches and updates the presented analysis after each batch. There are two analysis steps: First, protein alignments are calculated to determine which genera might be present in a sample. When strong evidence for a genus is found, then, in a second step, a more detailed analysis is performed by aligning the reads against the proteins of all species in the detected genus. The program presents a detailed analysis of species, antibiotic resistance genes, and virulence factors.