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

Bağci, C; Abrecht, B; Huson, DH

doi:10.1007/978-1-0716-3072-3_11

Item

ITEM ACTIONSEXPORT

Add to Basket

Local TagsRelease HistoryDetailsSummary

Released

Book Chapter

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

MPS-Authors

/persons/resource/persons271916

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

External Resource

No external resources are shared

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

There are no public fulltexts stored in PuRe

Supplementary Material (public)

There is no public supplementary material available

Citation

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

Abstract

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.