MEGAnnotator2: a pipeline for the assembly and annotation of microbial genomes.
Genomics
bioinformatics
next-generation sequencing
Journal
Microbiome research reports
ISSN: 2771-5965
Titre abrégé: Microbiome Res Rep
Pays: United States
ID NLM: 9918681186206676
Informations de publication
Date de publication:
2023
2023
Historique:
received:
23
12
2022
revised:
06
04
2023
accepted:
17
04
2023
medline:
7
12
2023
pubmed:
7
12
2023
entrez:
7
12
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 38058405
doi: 10.20517/mrr.2022.21
pmc: PMC10696586
doi:
Types de publication
Journal Article
Langues
eng
Pagination
15Informations de copyright
© The Author(s) 2023.
Déclaration de conflit d'intérêts
All authors declared that there are no conflicts of interest.
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