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Lugli et al. Microbiome Res Rep 2023;2:15 Microbiome Research
DOI: 10.20517/mrr.2022.21
Reports

Original Article Open Access

MEGAnnotator2: a pipeline for the assembly and
annotation of microbial genomes

1
1
1,2
2,3
1
Gabriele Andrea Lugli , Federico Fontana , Chiara Tarracchini , Christian Milani , Leonardo Mancabelli ,
1,2
Francesca Turroni , Marco Ventura 1,2,*
1
Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma,
Parma 43124, Italy.
2
Microbiome Research Hub, University of Parma, Parma 43124, Italy.
3
Department of Medicine and Surgery, University of Parma, Parma 43125, Italy.
Correspondence to: Marco Ventura, Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental
Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy. E-mail: marco.ventura@unipr.it
How to cite this article: Lugli GA, Fontana F, Tarracchini C, Milani C, Mancabelli L, Turroni F, Ventura M. MEGAnnotator2: a
pipeline for the assembly and annotation of microbial genomes. Microbiome Res Rep 2023;2:15.
https://dx.doi.org/10.20517/mrr.2022.21
Received: 23 Dec 2022 First Decision: 24 Mar 2023 Revised: 6 Apr 2023 Accepted: 17 Apr 2023 Published: 30 Apr 2023

Academic Editor: Rodolphe Barrangou Copy Editor: Ke-Cui Yang Production Editor: Ke-Cui Yang

Abstract
The reconstruction of microbial genome sequences by bioinformatic pipelines and the consequent functional
annotation of their genes’ repertoire are fundamental activities aiming at unveiling their biological mechanisms,
such as metabolism, virulence factors, and antimicrobial resistances. Here, we describe the development of the
MEGAnnotator2 pipeline able to manage all next-generation sequencing methodologies producing short- and long-
read DNA sequences. Starting from raw sequencing data, the updated pipeline can manage multiple analyses
leading to the assembly of high-quality genome sequences and the functional classification of their genetic
repertoire, providing the user with a useful report constituting features and statistics related to the microbial
genome. The updated pipeline is fully automated from the installation to the delivery of the output, thus requiring
minimal bioinformatics knowledge to be executed.

Keywords: Genomics, bioinformatics, next-generation sequencing

© The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0
International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing,
adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, as
long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and
indicate if changes were made.

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