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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References
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
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
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
Ciuffreda L, Rodríguez-Pérez H, Flores C (2021) Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J
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
Check Hayden E (2015) Pint-sized dna sequencer impresses first users. Nat News 521(7550):15
Albrecht B, Bağcı C, Huson DH (2020) MAIRA – real-time taxonomic and functional analysis of long reads on a laptop. BMC Bioinf 21(13):1–12
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59–60
Sheetlin SL, Park Y, Frith MC, Spouge JL (2014) Frameshift alignment: statistics and post-genomic applications. Bioinformatics 30(24):3575–3582
Commichaux S, Javkar K, Ramachandran P, Nagarajan N, Bertrand D, Chen Y, Reed E, Gonzalez-Escalona N, Strain E, Rand H, et al (2021). Evaluating the accuracy of listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads. BMC Genom 22(1):1–18
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, Hugenholtz P (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36(10):996–1004
Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33(suppl_1):D325–D328
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, et al (2016). CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res, gkw1004
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
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Bağcı, C., Albrecht, B., Huson, D.H. (2023). MAIRA: Protein-based Analysis of MinION Reads on a Laptop. In: Mitra, S. (eds) Metagenomic Data Analysis. Methods in Molecular Biology, vol 2649. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3072-3_11
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DOI: https://doi.org/10.1007/978-1-0716-3072-3_11
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