MAIRA - Highly efficient and accurate algorithms for mobile analysis of microbes

• Applicant: Professor Dr. Daniel H. Huson
• Subject Area: Bioinformatics and Theoretical Biology ; Parasitology and Biology of Tropical Infectious Disease Pathogens
• Term: from 2015 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 289436404

• Final Report Year: 2021

Final Report Abstract

The aim of this project was to develop new algorithms and software to support real-time analysis of mobile sequencing technologies. One main result of this work is an improved understanding of the challenges specific to the analysis of metagenomic long reads, such as the problem of frame shifts caused by sequencing errors. This has led to the development of new algorithms to address these challenges and the extension of the DIAMOND+MEGAN metagenomic analysis pipeline so as to accommodate long reads. A second main result is the development of the new MAIRA program, which runs on a laptop and processes the output of a MinION sequencing in real-time. We are currently exploring the use of MAIRA to monitor the dynamics of microbial communities in bioreactors. In future, the software will be extended to applications in genome mining. Moreover, we intend to deploy the software for in-field DNA analysis in situations in which access computational infrastructure is difficult.

Publications

• (2018). MEGAN-LR: New algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biology Direct, 13(6)
  DH Huson, B Albrecht, C Bagci, I Bessarab, A Gorska, D Jolic and RBH Williams
  (See online at https://doi.org/10.1186/s13062-018-0208-7)
• (2019). Annotated bacterial chromosomes from frame-shift-corrected long read metagenomic data. Microbiome, 7(61)
  K Arumugam, C Bagci, I Bessarab, S Beier, B Buchfink, A Gorska, G Qiu, DH Huson and RBH Williams
  (See online at https://doi.org/10.1186/s40168-019-0665-y)
• Introduction to the analysis of environmental sequences: Metagenomics with MEGAN, Evolutionary Genomics, Humana, New York, NY, 591-604 (2019)
  C Bagci, S Beier, A Gorska, DH Huson
  (See online at https://doi.org/10.1007/978-1-4939-9074-0_19)
• (2020) MAIRA-real-time taxonomic and functional analysis of long reads on a laptop, BMC Bioinformatics 21 (13), 1-12
  B Albrecht, C Bagci, DH Huson
  (See online at https://doi.org/10.1186/s12859-020-03684-2)
• (2021) DIAMOND+MEGAN: Fast and easy taxonomic and functional analysis of short and long microbiome sequences, Current Protocols, Volume 1, Issue 3
  C Bagci, S Patz, DH Huson
  (See online at https://doi.org/10.1002/cpz1.59)
• (2021) The isolate Caproiciproducens sp. 7D4C2 produces n-caproate at mildly acidic conditions from hexoses: genome and rBOX comparison with related strains and chain-elongating bacteria. Frontiers in Microbiology, Vol. 11, No. 594524
  S Esquivel-Elizondo, C Bagci, M Temovska, B Seung Jeon, I Bessarab, RBH Williams, DH Huson, LT Angenent
  (See online at https://doi.org/10.3389/fmicb.2020.594524)