Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023:2649:223-234.
doi: 10.1007/978-1-0716-3072-3_11.

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

Caner Bağcı  1   2 , Benjamin Albrecht  3 , Daniel H Huson  4
Affiliations

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

Caner Bağcı et al. Methods Mol Biol. 2023.

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.

Keywords: Functional profiling; Microbiome sequencing; Real-time analysis; Software; Taxonomic profiling.

PubMed Disclaimer

References

    1. Schmidt K, Mwaigwisya S, Crossman L, Doumith M, Munroe D, Pires C, Khan A, Woodford N, Saunders N, Wain J et al (2016) Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother 72(1):104–114 - DOI - PubMed
    1. Charalampous T, Kay GL, Richardson H, Aydin A, Baldan R, Jeanes C, Rae D, Grundy S, Turner DJ, Wain J, et al (2019) Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol 37(7):783–792 - DOI - PubMed
    1. Arumugam K, Bağcı C, Bessarab I, Beier S, Buchfink B, Gorska A, Qiu G, Huson DH, Williams RB (2019) Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data. Microbiome 7(1):1–13 - DOI
    1. Ciuffreda L, Rodríguez-Pérez H, Flores C (2021) Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J
    1. Huson DH, Albrecht B, Bağcı C, Bessarab I, Gorska A, Jolic D, Williams RB (2018) MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biol. Direct 13(1):1–17 - DOI

LinkOut - more resources