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.

2. Loman NJ, Pallen MJ. Twenty years of bacterial genome sequencing. Nat Rev Microbiol 2015;13:787-94.

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.

4. Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol 2021;82:801-11.

5. Slatko BE, Gardner AF, Ausubel FM. Overview of next-generation sequencing technologies. Curr Protoc Mol Biol 2018;122:e59.

6. Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The third revolution in sequencing technology. Trends Genet 2018;34:666-81.

7. Sohn JI, Nam JW. The present and future of de novo whole-genome assembly. Brief Bioinform 2018;19:23-40.

8. Kingsford C, Schatz MC, Pop M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinform 2010;11:21.

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.

10. Sallet E, Gouzy J, Schiex T. EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes. Bioinformatics 2014;30:2659-61.

11. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068-9.

12. Tatusova T, DiCuccio M, Badretdin A, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:6614-24.

13. Ruiz-Perez CA, Conrad RE, Konstantinidis KT. MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. BMC Bioinform 2021;22:11.

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.

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.

16. Ejigu GF, Jung J. Review on the computational genome annotation of sequences obtained by next-generation sequencing. Biology 2020;9:295.

17. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012;28:3150-2.

18. Brown C, Irber L. sourmash: a library for MinHash sketching of DNA. JOSS 2016;1:27.

19. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013;41:D590-6.

20. Caspi R, Billington R, Keseler IM, et al. The MetaCyc database of metabolic pathways and enzymes - a 2019 update. Nucleic Acids Res 2020;48:D445-53.

21. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 2009;25:1754-60.

22. Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455-77.

23. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017;27:722-36.

24. Wick RR, Holt KE. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol 2022;18:e1009802.

25. Chen Y, Ye W, Zhang Y, Xu Y. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res 2015;43:7762-8.

26. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018;9:5114.

27. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25:1043-55.

28. Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics 2009;25:2071-3.

29. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 2010;11:119.

30. Dimonaco NJ, Aubrey W, Kenobi K, Clare A, Creevey CJ. No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study. Bioinformatics 2022;38:1198-207.

31. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015;12:59-60.

32. Jones P, Binns D, Chang HY, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 2014;30:1236-40.

33. Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021;49:9077-96.

34. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012;28:464-9.

35. Zhang P, Jiang D, Wang Y, Yao X, Luo Y, Yang Z. Comparison of de novo assembly strategies for bacterial genomes. Int J Mol Sci 2021;22:7668.