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. 2020 Sep 17;21(Suppl 13):390.
doi: 10.1186/s12859-020-03684-2.

MAIRA- real-time taxonomic and functional analysis of long reads on a laptop

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

MAIRA- real-time taxonomic and functional analysis of long reads on a laptop

Benjamin Albrecht et al. BMC Bioinformatics. .

Abstract

Background: Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually designed to run on servers and in the cloud.

Results: MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop, without requiring external resources. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph.

Conclusions: We envision this software being used by researchers in the field, when access to servers or cloud facilities is difficult, or by individuals that do not routinely access such facilities, such as medical researchers, crop scientists, or teachers.

Keywords: Antibiotic resistance; Functional analysis; Long read sequencing; Metagenomics; Microbiome; Mobile computing; Open source software; Taxonomic analysis; Virulence factors.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
MAIRA workflow. In an online manner, a batches of long reads obtained from a sequencing device are subjected to protein alignment against a precomputed database of genus-specific marker genes. Based on this, b the list of detected genera is updated in real-time. c Substantial evidence for the presence of a specific genus triggers d batch-wise protein alignment against a full database of proteins associated with the genus. Based on this, a protein graph is updated and used to perform species and-strain level analysis of the long reads, including the identification of antibiotic resistance and virulence factors
Fig. 2
Fig. 2
Performance on mock community. a The presence score for true positive (green) and false positive (red) genera as a function of computation time and number of reads processed. The blue line indicates the threshold used to deem a genus “present”. b The completeness of true positive (green) and false positive (red) species as a function of computation time and number of reads processed. The blue line indicates the threshold used to deem a species “present”. c The coverage of species, as a function of time and number of reads processed
Fig. 3
Fig. 3
MAIRA user interface. During processing of an input file or directory, MAIRA provides an overview of the genera, species and functional classes discovered so far. The user can explore and download results while they are being produced, so as to allow insights into the processed sequences
See this image and copyright information in PMC

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