MAIRA- real-time taxonomic and functional analysis of long reads on a laptop
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RESEARCH
Open Access
MAIRA- real-time taxonomic and functional analysis of long reads on a laptop ˘ 1,2† and Daniel H. Huson1* Benjamin Albrecht1† , Caner Bagcı From The 18th Asia Pacific Bioinformatics Conference Seoul, Korea. 18–20 August 2020 *Correspondence: [email protected] † Benjamin Albrecht and Caner ˘ contributed equally to this Bagcı work. 1 Department of Computer Science, University of Tübingen, Sand 14, Tübingen, Germany Full list of author information is available at the end of the article
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: Metagenomics, Microbiome, Long read sequencing, Taxonomic analysis, Functional analysis, Mobile computing, Open source software, Antibiotic resistance, Virulence factors
Background The Oxford Nanopore MinION USB sequencing device, the MinIT USB base-calling device and advances in lab-on-a-chip technologies allow sequencing to be taken into field [1]. With ever rising sequencing yield and continuously growing reference databases, the computational analysis of such data is challenging, and much work is being done to address this efficiently, usually on a server or using cloud computing [2, 3]. Modern laptops provide a lot of computational power, main memory and fast access to SSD storage, and thus it should be possible to perform detailed analysis of microbiome sequencing data in the field, on a laptop.
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