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Lugli et al. Microbiome Res Rep 2023;2:15 https://dx.doi.org/10.20517/mrr.2022.21 Page 15 of 16
Data curation and data analysis: Fontana F, Tarracchini C, Milani C, Mancabelli L
Supervision and manuscript editing: Turroni F, Ventura M
Availability of data and materials
The MEGAnnotator2 pipeline is downloadable at http://probiogenomics.unipr.it/cmu/. The installer file
can be retrieved under the “Software & Tools” drop-down menu, section “MEGAnnotator2”, button
“Download MEGAnnotator2”. In the same section, the manual can be downloaded using the button
“Download Manual”.
Financial support and sponsorship
Not applicable.
Conflicts of interest
All authors declared that there are no conflicts of interest.
Ethical approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Copyright
© The Author(s) 2023.
REFERENCES
1. Fleischmann RD, Adams MD, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Science 1995;269:496-512. DOI
2. Loman NJ, Pallen MJ. Twenty years of bacterial genome sequencing. Nat Rev Microbiol 2015;13:787-94. DOI PubMed
3. Segerman B. The most frequently used sequencing technologies and assembly methods in different time segments of the bacterial
surveillance and RefSeq genome databases. Front Cell Infect Microbiol 2020;10:527102. DOI PubMed PMC
4. Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol 2021;82:801-11. DOI
PubMed
5. Slatko BE, Gardner AF, Ausubel FM. Overview of next-generation sequencing technologies. Curr Protoc Mol Biol 2018;122:e59.
DOI PubMed PMC
6. Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The third revolution in sequencing technology. Trends Genet 2018;34:666-81. DOI
PubMed
7. Sohn JI, Nam JW. The present and future of de novo whole-genome assembly. Brief Bioinform 2018;19:23-40. DOI PubMed
8. Kingsford C, Schatz MC, Pop M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinform 2010;11:21. DOI
PubMed PMC
9. Schmid M, Frei D, Patrignani A, et al. Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring
very long, near identical repeats. Nucleic Acids Res 2018;46:8953-65. DOI PubMed PMC
10. Sallet E, Gouzy J, Schiex T. EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes. Bioinformatics
2014;30:2659-61. DOI PubMed
11. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068-9. DOI PubMed
12. Tatusova T, DiCuccio M, Badretdin A, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:6614-24. DOI
PubMed PMC
13. Ruiz-Perez CA, Conrad RE, Konstantinidis KT. MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for
microbial genomes. BMC Bioinform 2021;22:11. DOI PubMed PMC
14. Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M. MEGAnnotator: a user-friendly pipeline for microbial genomes
assembly and annotation. FEMS Microbiol Lett 2016;363:fnw049. DOI PubMed
15. Wu Y, Zheng Y, Wang S, et al. Genetic divergence and functional convergence of gut bacteria between the Eastern honey bee Apis
cerana and the Western honey bee Apis mellifera. J Adv Res 2022;37:19-31. DOI PubMed PMC
16. Ejigu GF, Jung J. Review on the computational genome annotation of sequences obtained by next-generation sequencing. Biology