Al Yami, S. and Huang, C.-H., 2019. LFastqC: A lossless non-reference-based FASTQ compressor. PLoS One 14, e0224806. https://doi.org/10.1371/journal.pone.0224806 

Bayat, A., 2002. Science, medicine, and the future: Bioinformatics. BMJ 324, 1018–1022. https://doi.org/10.1136/bmj.324.7344.1018

Blazej, R. G., Kumaresan, P., Mathies, R. A., 2006. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing. Proc. Natl. Acad. Sci. U. S. A. 103, 7240–7245. https://doi.org/10.1073/pnas.0602476103

Boris, K. V., Ryzhova, N. N., Kochieva, E. Z., 2011. Identification and characterization of intraspecific variability of the sucrose synthase gene Sus4 of potato (Solanum tuberosum). Russ. J. Genet. 47, 168–175. https://doi.org/10.1134/S1022795411020074

Brown, C.L., Keenum, I.M., Dai, D., Zhang, L., Vikesland, P.J., Pruden, A., 2021. Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes. Sci. Rep. 11, 3753. https://doi.org/10.1038/s41598-021-83081-8

Chaisson, M.J., Pevzner, P.A., 2008. Short read fragment assembly of bacterial genomes. Genome Res. 18, 324–330. https://doi.org/10.1101/gr.7088808

Chao, J., Tang, F., Xu, L., 2022. Developments in Algorithms for Sequence Alignment: A Review. Biomolecules 12. https://doi.org/10.3390/biom12040546

Chen, Y., Ye, W., Zhang, Y., Xu, Y., 2015. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res. 43, 7762–7768. https://doi.org/10.1093/nar/gkv784

Cheng, Q.-Q., Ouyang, Y., Tang, Z.-Y., Lao, C.-C., Zhang, Y.-Y., Cheng, C.-S., Zhou, H., 2021. Review on the Development and Applications of Medicinal Plant Genomes. Front. Plant Sci. 12, 791219. https://doi.org/10.3389/fpls.2021.791219

Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., Turner, S.W., Korlach, J., 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569. https://doi.org/10.1038/nmeth.2474

Dash, S., Rahman, S.R., Hines, H.M., Feng, W., 2021. iBLAST: Incremental BLAST of new sequences via automated e-value correction. PLoS One 16, e0249410. https://doi.org/10.1371/journal.pone.0249410

Delsuc, F., Brinkmann, H., Philippe, H., 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6, 361–375. https://doi.org/10.1038/nrg1603

Edwards, D., Batley, J., 2010. Plant genome sequencing: applications for crop improvement. Plant Biotechnol. J. 8, 2–9.  https://doi.org/10.1111/j.1467-7652.2009.00459.x

Eric, S.D., Nicholas, T.K.D.D., Theophilus, K.A., 2014. Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA). J. Bioinforma. Seq. Anal. 6, 1–6. https://doi.org/10.5897/ijbc2013.0086

Genereux, D.P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V.D., Murén, E., Juan, D., Bejerano, G., Casewell, N.R., Chemnick, L.G., Damas, J., Di Palma, F., Diekhans, M., Fiddes, I.T., Garber, M., Gladyshev, V.N., Goodman, L., Haerty, W., Houck, M.L., Hubley, R., Kivioja, T., Koepfli, K.-P., Kuderna, L.F.K., Lander, E.S., Meadows, J.R.S., Murphy, W.J., Nash, W., Noh, H.J., Nweeia, M., Pfenning, A.R., Pollard, K.S., Ray, D.A., Shapiro, B., Smit, A.F.A., Springer, M.S., Steiner, C.C., Swofford, R., Taipale, J., Teeling, E.C., Turner-Maier, J., Alfoldi, J., Birren, B., Ryder, O.A., Lewin, H.A., Paten, B., Marques-Bonet, T., Lindblad-Toh, K., Karlsson, E.K., Consortium, Z., 2020. A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240–245. https://doi.org/10.1038/s41586-020-2876-6

Goff, S.A., Ricke, D., Lan, T.-H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B.M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W., Chen, L., Cooper, B., Park, S., Wood, T.C., Mao, L., Quail, P., Wing, R., Dean, R., Yu, Y., Zharkikh, A., Shen, R., Sahasrabudhe, S., Thomas, A., Cannings, R., Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R.M., Bhatnagar, S., Adey, N., Rubano, T., Tusneem, N., Robinson, R., Feldhaus, J., Macalma, T., Oliphant, A., Briggs, S., 2002. A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica). Science (80-.). 296, 92–100. https://doi.org/10.1126/science.1068275

He, M., Chi, X., Ren, J., 2021. Applications of Oxford Nanopore Sequencing in Schizosaccharomyces pombe. Methods Mol. Biol. 2196, 97–116. https://doi.org/10.1007/978-1-0716-0868-5_9

Heather, J.M., Chain, B., 2016. The sequence of sequencers: The history of sequencing DNA. Genomics 107, 1–8. https://doi.org/10.1016/j.ygeno.2015.11.003

Henry, R.J., 2022. Progress in Plant Genome Sequencing. Appl. Biosci. 1, 113–128. https://doi.org/10.3390/applbiosci1020008

Initiative, T.A.G., 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815. https://doi.org/10.1038/35048692

Jain, M., Olsen, H.E., Paten, B., Akeson, M., 2016. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239. https://doi.org/10.1186/s13059-016-1103-0

Keerthana, P., Gochhait, S., 2022. Application of Bioinformatics in Health Care and Medicine BT - Information Retrieval in Bioinformatics: A Practical Approach, in: Dutta, S., Gochhait, S. (Eds.),. Springer Nature Singapore, Singapore, pp. 83–99. https://doi.org/10.1007/978-981-19-6506-7_5

Kress, W.J., Soltis, D.E., Kersey, P.J., Wegrzyn, J.L., Leebens-Mack, J.H., Gostel, M.R., Liu, X., Soltis, P.S., 2022. Green plant genomes: What we know in an era of rapidly expanding opportunities. Proc. Natl. Acad. Sci. U. S. A. 119, 1–9. https://doi.org/10.1073/pnas.2115640118

Kwon, Y.W., Jo, H.S., Bae, S., Seo, Y., Song, P., Song, M., Yoon, J.H., 2021. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front. Med. 8, 1–18. https://doi.org/10.3389/fmed.2021.747333

Li, H., Yang, Y., Hong, W., Huang, M., Wu, M., Zhao, X., 2020. Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduct. Target. Ther. 5, 1. https://doi.org/10.1038/s41392-019-0089-y

Marx, V., 2021. Long road to long-read assembly. Nat. Methods 18, 125–129. https://doi.org/10.1038/s41592-021-01057-y

McGinnis, S., Madden, T.L., 2004. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32, W20-5. https://doi.org/10.1093/nar/gkh435

Mignardi, M., Nilsson, M., 2014. Fourth-generation sequencing in the cell and the clinic. Genome Med. 6, 31. https://doi.org/10.1186/gm548

Miller, J.R., Zhou, P., Mudge, J., Gurtowski, J., Lee, H., Ramaraj, T., Walenz, B.P., Liu, J., Stupar, R.M., Denny, R., Song, L., Singh, N., Maron, L.G., McCouch, S.R., McCombie, W.R., Schatz, M.C., Tiffin, P., Young, N.D., Silverstein, K.A.T., 2017. Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics 18, 541. https://doi.org/10.1186/s12864-017-3927-8

Mu, H., Wang, B., Yuan, F., 2022. Bioinformatics in Plant Breeding and Research on Disease Resistance. Plants 11. https://doi.org/10.3390/plants11223118

Nagarajan, N., Pop, M., 2013. Sequence assembly demystified. Nat. Rev. Genet. 14, 157–167. https://doi.org/10.1038/nrg3367

Ong, Q., Nguyen, P., Phuong Thao, N., Le, L., 2016. Bioinformatics Approach in Plant Genomic Research. Curr. Genomics 17, 368–378. https://doi.org/10.2174/1389202917666160331202956

Pandey, R.V., Pabinger, S., Kriegner, A., Weinhäusel, A., 2016. ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research. BMC Bioinformatics 17, 56. https://doi.org/10.1186/s12859-016-0915-y

Pearson, W.R., 2016. Finding Protein and Nucleotide Similarities with FASTA. Curr. Protoc. Bioinforma. 53, 3.9.1-3.9.25. https://doi.org/10.1002/0471250953.bi0309s53

Pemmasani, S.K., Raman, R., Mohapatra, R., Vidyasagar, M., Acharya, A., 2020. A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation. Front. Genet. 11, 1–7. https://doi.org/10.3389/fgene.2020.00753

Pereira, R., Oliveira, J., Sousa, M., 2020. Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics. J. Clin. Med. 9. https://doi.org/10.3390/jcm9010132

Pertsemlidis, A., Fondon, J.W., 2001. Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol. 2, reviews2002.1. https://doi.org/10.1186/gb-2001-2-10-reviews2002

Posey, J.E., 2019. Genome sequencing and implications for rare disorders. Orphanet J. Rare Dis. 14, 153. https://doi.org/10.1186/s13023-019-1127-0

Prjibelski, A.D., Korobeynikov, A.I., Lapidus, A.L., 2018. Sequence analysis, Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics. https://doi.org/10.1016/B978-0-12-809633-8.20106-4

Rhee, S.Y., Dickerson, J., Xu, D., 2006. Bioinformatics and its applications in plant biology. Annu. Rev. Plant Biol. 57, 335–360. https://doi.org/10.1146/annurev.arplant.56.032604.144103

Roberts, R.J., Carneiro, M.O., Schatz, M.C., 2013. The advantages of SMRT sequencing. Genome Biol. 14, 405. https://doi.org/10.1186/gb-2013-14-7-405

?ahin, E.Ç., Ayd?n, Y., Gilles, T., Uncuo?lu, A.A., Lucas, S.J., 2022. Chapter 28 - Concepts and applications of bioinformatics for sustainable agriculture, in: Sharma, P., Yadav, D., Gaur, R.K.B.T.-B. in A. (Eds.),. Academic Press, pp. 455–489. https://doi.org/10.1016/B978-0-323-89778-5.00012-X

Salazar Robles, G., Hernández, L.R., Pedraza Pérez, Y., Juárez, Z.N., Rodríguez Acosta, M., Pérez Armendáriz, B., Bautista Rodríguez, E., El Kassis, E.G., 2022. Bioinformatic approach for the identification of plant species that accumulate palmitoleic acid. Electron. J. Biotechnol. 60, 58–69. https://doi.org/10.1016/j.ejbt.2022.09.008

Salzberg, S.L., 2019. Next-generation genome annotation: we still struggle to get it right. Genome Biol. 20, 92. https://doi.org/10.1186/s13059-019-1715-2

Slatko, B.E., Gardner, A.F., Ausubel, F.M., 2018. Overview of Next-Generation Sequencing Technologies. Curr. Protoc. Mol. Biol. 122, e59. https://doi.org/10.1002/cpmb.59

Stein, L., 2001. Genome annotation: from sequence to biology. Nat. Rev. Genet. 2, 493–503. https://doi.org/10.1038/35080529

Supplitt, S., Karpinski, P., Sasiadek, M., Laczmanska, I., 2021. Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine. Int. J. Mol. Sci. 22. https://doi.org/10.3390/ijms22031422

Suriyakala, G., Sathiyaraj, S., Gandhi, A.D., Vadakkan, K., Mahadeva Rao, U.S., Babujanarthanam, R., 2021. Plumeria pudica Jacq. flower extract - mediated silver nanoparticles: Characterization and evaluation of biomedical applications. Inorg. Chem. Commun. 126, 108470. https://doi.org/10.1016/j.inoche.2021.108470

Theys, K., Lemey, P., Vandamme, A., Baele, G., 2019. Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases 7, 1–18. https://doi.org/10.3389/fpubh.2019.00208

Thompson, J.D., Linard, B., Lecompte, O., Poch, O., 2011. A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives. PLoS One 6, e18093. https://doi.org/10.1371/journal.pone.0018093

Vadakkan, K., 2019. Acute and sub-acute toxicity study of bacterial signaling inhibitor Solanum torvum root extract in Wister rats. Clin. Phytoscience 5. https://doi.org/10.1186/s40816-019-0113-3

Vadakkan, K., Cheruvathur, M.K., Chulliparambil, A.S., Francis, F., Abimannue, A.P., 2021. Proteolytic enzyme arbitrated antagonization of helminthiasis by Cinnamomum cappara leaf extract in Pheretima posthuma. Clin. Phytoscience 7, 23. https://doi.org/10.1186/s40816-021-00261-9

Vadakkan, K., Hemapriya, J., Selvaraj, V., 2019a. Quorum quenching intervened in vivo attenuation and immunological clearance enhancement by Solanum torvum root extract against Pseudomonas aeruginosa instigated pneumonia in Sprague Dawley rats. Clin Phytosci 5, 24 (2019). https://doi.org/10.1186/s40816-019-0120-4

Vadakkan, K., Vijayanand, S., Choudhury, A.A., Gunasekaran, R., Hemapriya, J., 2018. Optimization of quorum quenching mediated bacterial attenuation of Solanum torvum root extract by response surface modelling through Box-Behnken approach. J. Genet. Eng. Biotechnol. 16, 381–386. https://doi.org/10.1016/j.jgeb.2018.02.001

Vadakkan, K., Vijayanand, S., Hemapriya, J., Gunasekaran, R., 2019b. Quorum sensing inimical activity of Tribulus terrestris against gram negative bacterial pathogens by signalling interference. 3 Biotech 9, 163. https://doi.org/10.1007/s13205-019-1695-7

Wang, Y., Wu, H., Cai, Y., 2018. A benchmark study of sequence alignment methods for protein clustering. BMC Bioinformatics 19, 529. https://doi.org/10.1186/s12859-018-2524-4

Wang, Yunhao, Zhao, Y., Bollas, A., Wang, Yuru, Au, K.F., 2021. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348–1365. https://doi.org/10.1038/s41587-021-01108-x

Wei, L., Liu, Y., Dubchak, I., Shon, J., Park, J., 2002. Comparative genomics approaches to study organism similarities and differences. J. Biomed. Inform. 35, 142–150. https://doi.org/10.1016/s1532-0464(02)00506-3

Wingett, S.W., Andrews, S., 2018. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Research 7, 1338. https://doi.org/10.12688/f1000research.15931.2

Wittich, H.C., Seeland, M., Wäldchen, J., Rzanny, M., Mäder, P., 2018. Recommending plant taxa for supporting on-site species identification. BMC Bioinformatics 19, 190. https://doi.org/10.1186/s12859-018-2201-7

Xiao, T., Zhou, W., 2020. The third generation sequencing: the advanced approach to genetic diseases. Transl. Pediatr. 9, 163–173. https://doi.org/10.21037/tp.2020.03.06

Ying, Y.-L., Hu, Z.-L., Zhang, S., Qing, Y., Fragasso, A., Maglia, G., Meller, A., Bayley, H., Dekker, C., Long, Y.-T., 2022. Nanopore-based technologies beyond DNA sequencing. Nat. Nanotechnol. 17, 1136–1146. https://doi.org/10.1038/s41565-022-01193-2