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

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.

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 Creators:
Bağci, C1, Author                 
Abrecht, B, Author
Huson, DH, Author                 
Affiliations:
1IMPRS From Molecules to Organisms, Max Planck Institute for Biology Tübingen, Max Planck Society, ou_3376132              

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 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.

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 Dates: 2023
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1007/978-1-0716-3072-3_11
PMID: 37258865
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Title: Metagenomic Data Analysis
Source Genre: Book
 Creator(s):
Mitra, S, Editor
Affiliations:
-
Publ. Info: NewYork, NY, USA : Humana Press
Pages: 441 Volume / Issue: - Sequence Number: - Start / End Page: 223 - 234 Identifier: ISBN: 978-1-0716-3071-6
DOI: 10.1007/978-1-0716-3072-3

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Title: Methods in Molecular Biology
  Other : Methods Mol. Biol.
Source Genre: Series
 Creator(s):
Affiliations:
Publ. Info: US : Springer
Pages: - Volume / Issue: 2649 Sequence Number: - Start / End Page: - Identifier: ISSN: 1064-3745
CoNE: https://pure.mpg.de/cone/journals/resource/954927725544