Benjamin Albrecht1, Caner Bağcı1,2, Daniel H Huson3. 1. Department of Computer Science, University of Tübingen, Sand 14, Tübingen, Germany. 2. International Max Planck Research School From Molecules to Organisms, Max Planck Institute for Developmental Biology and Eberhard Karls University Tübingen, Max-Planck-Ring 5, Tübingen, 72076, Germany. 3. Department of Computer Science, University of Tübingen, Sand 14, Tübingen, Germany. daniel.huson@uni-tuebingen.de.
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.
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.
Entities:
Keywords:
Antibiotic resistance; Functional analysis; Long read sequencing; Metagenomics; Microbiome; Mobile computing; Open source software; Taxonomic analysis; Virulence factors
Authors: Baofeng Jia; Amogelang R Raphenya; Brian Alcock; Nicholas Waglechner; Peiyao Guo; Kara K Tsang; Briony A Lago; Biren M Dave; Sheldon Pereira; Arjun N Sharma; Sachin Doshi; Mélanie Courtot; Raymond Lo; Laura E Williams; Jonathan G Frye; Tariq Elsayegh; Daim Sardar; Erin L Westman; Andrew C Pawlowski; Timothy A Johnson; Fiona S L Brinkman; Gerard D Wright; Andrew G McArthur Journal: Nucleic Acids Res Date: 2016-10-26 Impact factor: 16.971
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