{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:28:54Z","timestamp":1760059734813,"version":"build-2065373602"},"reference-count":111,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T00:00:00Z","timestamp":1751587200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Portuguese Foundation for Science and Technology (FCT)","doi-asserted-by":"publisher","award":["UIDB\/00709\/2020","CENTRO-08-5864-FSE-000039"],"award-info":[{"award-number":["UIDB\/00709\/2020","CENTRO-08-5864-FSE-000039"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014717","name":"Programa Operacional Regional do Centro","doi-asserted-by":"publisher","award":["UIDB\/00709\/2020","CENTRO-08-5864-FSE-000039"],"award-info":[{"award-number":["UIDB\/00709\/2020","CENTRO-08-5864-FSE-000039"]}],"id":[{"id":"10.13039\/501100014717","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Technologies"],"abstract":"<jats:p>Introduction: Bioinformatics is a relatively recent multidisciplinary research field continuously offering novel opportunities. Although many researchers are actively working in\/with bioinformatics, some research centers still face difficulties in hiring bioinformaticians and establishing the appropriate (first) bioinformatics infrastructures and computational resources. In our research center, we started from scratch and established initial bioinformatics infrastructures for common use and also for the specific case of precision\/personalized medicine. Case description: Here, we report a case study reflecting our specific needs and circumstances during the implementation of a novel bioinformatics laboratory. This involved the preparation of rooms, computer networks, computational resources novel designs, and upgrades to existing designs. Moreover, this work involved people from diverse areas and institutions, such as companies, institutional projects, informatics, and technical infrastructures services. Discussion and evaluation: The work resulted in the implementation of four novel designs dedicated to genomic medicine and in the adaptation of two existing designs dedicated to common use located in the dry-lab room. This is not an accurate and objective work, as it often depends on the available computer hardware and the target bioinformatics field(s). The four novel designs offered substantial improvements when compared to the upgraded designs, additionally corroborated by performance evaluations, which resulted in an overall highest performance of the novel designs. Conclusions: We present work that was developed over two years until completion with functioning infrastructure. This project enabled us to learn many novel aspects not only related to redundant disk technologies, but also related to computer networks, hardware, storage-management operating systems, file systems, performance evaluation, and also in the management of services. Moreover, additional equipment will be important to maintain and expand the potential and reliability of the bioinformatics laboratory. We hope that this work can be helpful for other researchers seeking to design their bioinformatics equipment or laboratories.<\/jats:p>","DOI":"10.3390\/technologies13070285","type":"journal-article","created":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T04:51:17Z","timestamp":1751604677000},"page":"285","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Computational Resources and Infrastructures for a Novel Bioinformatics Laboratory: A Case Study"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0084-6116","authenticated-orcid":false,"given":"Emanuel","family":"Maldonado","sequence":"first","affiliation":[{"name":"RISE-Health, Department of Medical Sciences, Faculty of Health Sciences, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilh\u00e3, Portugal"},{"name":"CICS-UBI\u2014Health Sciences Research Center, University of Beira Interior, 6201-506 Covilh\u00e3, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9326-8900","authenticated-orcid":false,"given":"Manuel C.","family":"Lemos","sequence":"additional","affiliation":[{"name":"RISE-Health, Department of Medical Sciences, Faculty of Health Sciences, University of Beira Interior, Av. Infante D. Henrique, 6200-506 Covilh\u00e3, Portugal"},{"name":"CICS-UBI\u2014Health Sciences Research Center, University of Beira Interior, 6201-506 Covilh\u00e3, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/35042090","article-title":"The Origins of Bioinformatics","volume":"1","author":"Hagen","year":"2000","journal-title":"Nat. Rev. Genet."},{"doi-asserted-by":"crossref","unstructured":"Hogeweg, P. (2011). The Roots of Bioinformatics in Theoretical Biology. PLoS Comput. Biol., 7.","key":"ref_2","DOI":"10.1371\/journal.pcbi.1002021"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1093\/bib\/bbx144","article-title":"Precision Medicine Needs Pioneering Clinical Bioinformaticians","volume":"20","author":"Dopazo","year":"2019","journal-title":"Brief. Bioinform."},{"doi-asserted-by":"crossref","unstructured":"Lewitter, F., Rebhan, M., Richter, B., and Sexton, D. (2009). The Need for Centralization of Computational Biology Resources. PLOS Comput. Biol., 5.","key":"ref_4","DOI":"10.1371\/journal.pcbi.1000372"},{"unstructured":"(2024, June 13). University of Beira Interior CICS-UBI Health Sciences Research Center, University of Beira Interior. Available online: https:\/\/www.ubi.pt\/sites\/cics\/en.","key":"ref_5"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"494","DOI":"10.5195\/jmla.2018.512","article-title":"High-Performance Computing Service for Bioinformatics and Data Science","volume":"106","author":"Courneya","year":"2018","journal-title":"J. Med. Libr. Assoc."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s13167-024-00353-9","article-title":"Promoting Advanced Medical Services in the Framework of 3PM\u2014A Proof-of-Concept by the \u201cCentro\u201d Region of Portugal","volume":"15","author":"Regateiro","year":"2024","journal-title":"EPMA J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s40537-022-00681-5","article-title":"The Power of Big Data Mining to Improve the Health Care System in the United Arab Emirates","volume":"10","author":"Alhajaj","year":"2023","journal-title":"J. Big Data"},{"doi-asserted-by":"crossref","unstructured":"Kong, D., Yu, H., Sim, X., White, K., Tai, E.S., Wenk, M., and Teo, A.K.K. (2022). Multidisciplinary Effort to Drive Precision-Medicine for the Future. Front. Digit. Health, 4.","key":"ref_9","DOI":"10.3389\/fdgth.2022.845405"},{"doi-asserted-by":"crossref","unstructured":"Petersen, B.-S., Fredrich, B., Hoeppner, M.P., Ellinghaus, D., and Franke, A. (2017). Opportunities and Challenges of Whole-Genome and -Exome Sequencing. BMC Genet., 18.","key":"ref_10","DOI":"10.1186\/s12863-017-0479-5"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1186\/s13073-016-0388-7","article-title":"Reconciling Evidence-Based Medicine and Precision Medicine in the Era of Big Data: Challenges and Opportunities","volume":"8","author":"Beckmann","year":"2016","journal-title":"Genome Med."},{"doi-asserted-by":"crossref","unstructured":"Alyass, A., Turcotte, M., and Meyre, D. (2015). From Big Data Analysis to Personalized Medicine for All: Challenges and Opportunities. BMC Med. Genom., 8.","key":"ref_12","DOI":"10.1186\/s12920-015-0108-y"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.gheart.2017.01.005","article-title":"Development of Bioinformatics Infrastructure for Genomics Research","volume":"12","author":"Mulder","year":"2017","journal-title":"Glob. Heart"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.margen.2016.04.012","article-title":"Next-Generation Biology: Sequencing and Data Analysis Approaches for Non-Model Organisms","volume":"30","author":"Albrechtsen","year":"2016","journal-title":"Mar. Genom."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.jbi.2013.07.001","article-title":"\u2018Big Data\u2019, Hadoop and Cloud Computing in Genomics","volume":"46","author":"Daugelaite","year":"2013","journal-title":"J. Biomed. Inform."},{"unstructured":"Maldonado, E. (2020). Bioinformatics Applications for Optimizing Downstream Analyses in Evolutionary Genomics. [Ph.D. Thesis, Faculty of Sciences, University of Porto]. Available online: https:\/\/hdl.handle.net\/10216\/127527.","key":"ref_16"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"CIN.S13779","DOI":"10.4137\/CIN.S13779","article-title":"Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing","volume":"13","author":"Bao","year":"2014","journal-title":"Cancer Inform."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1111\/nyas.13281","article-title":"Big Data Access and Infrastructure for Modern Biology: Case Studies in Data Repository Utility","volume":"1387","author":"Boles","year":"2017","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1724","DOI":"10.1093\/bioinformatics\/btv061","article-title":"Omics Pipe: A Community-Based Framework for Reproducible Multi-Omics Data Analysis","volume":"31","author":"Fisch","year":"2015","journal-title":"Bioinformatics"},{"doi-asserted-by":"crossref","unstructured":"Hasin, Y., Seldin, M., and Lusis, A. (2017). Multi-Omics Approaches to Disease. Genome Biol., 18.","key":"ref_20","DOI":"10.1186\/s13059-017-1215-1"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.cell.2012.02.009","article-title":"Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes","volume":"148","author":"Chen","year":"2012","journal-title":"Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nrg2795","article-title":"Next-Generation Genomics: An Integrative Approach","volume":"11","author":"Hawkins","year":"2010","journal-title":"Nat. Rev. Genet."},{"doi-asserted-by":"crossref","unstructured":"Shi, L., and Wang, Z. (2019). Computational Strategies for Scalable Genomics Analysis. Genes, 10.","key":"ref_23","DOI":"10.3390\/genes10121017"},{"doi-asserted-by":"crossref","unstructured":"Stephens, Z.D., Lee, S.Y., Faghri, F., Campbell, R.H., Zhai, C., Efron, M.J., Iyer, R., Schatz, M.C., Sinha, S., and Robinson, G.E. (2015). Big Data: Astronomical or Genomical?. PLoS Biol., 13.","key":"ref_24","DOI":"10.1371\/journal.pbio.1002195"},{"unstructured":"(2024, October 04). Intel CPU vs. GPU: What\u2019s the Difference?. Available online: https:\/\/www.intel.com\/content\/www\/us\/en\/products\/docs\/processors\/cpu-vs-gpu.html.","key":"ref_25"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"044130","DOI":"10.1063\/5.0014475","article-title":"Scalable Molecular Dynamics on CPU and GPU Architectures with NAMD","volume":"153","author":"Phillips","year":"2020","journal-title":"J. Chem. Phys."},{"doi-asserted-by":"crossref","unstructured":"Ahmad, T., Ahmed, N., Al-Ars, Z., and Hofstee, H.P. (2020). Optimizing Performance of GATK Workflows Using Apache Arrow In-Memory Data Framework. BMC Genom., 21.","key":"ref_27","DOI":"10.1186\/s12864-020-07013-y"},{"unstructured":"Maldonado, E. (2024, June 18). MMAP: Multi-Core Method for Analysis Pipelines. Available online: https:\/\/mymmap.sourceforge.io\/.","key":"ref_28"},{"doi-asserted-by":"crossref","unstructured":"Maldonado, E., and Antunes, A. (2019). LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation. BMC Bioinform., 20.","key":"ref_29","DOI":"10.1186\/s12859-019-3292-5"},{"doi-asserted-by":"crossref","unstructured":"Maldonado, E., Almeida, D., Escalona, T., Khan, I., Vasconcelos, V., and Antunes, A. (2016). LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinform., 17.","key":"ref_30","DOI":"10.1186\/s12859-016-1204-5"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"giae060","DOI":"10.1093\/gigascience\/giae060","article-title":"Design and Implementation of a Scalable High-Performance Computing (HPC) Cluster for Omics Data Analysis: Achievements, Challenges and Recommendations in LMICs","volume":"13","author":"Ghedira","year":"2024","journal-title":"GigaScience"},{"doi-asserted-by":"crossref","unstructured":"Jambulingam, D., Rathinakannan, V.S., Heron, S., Schleutker, J., and Fey, V. (2024). Kuura\u2014An Automated Workflow for Analyzing WES and WGS Data. PLoS ONE, 19.","key":"ref_32","DOI":"10.1371\/journal.pone.0296785"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"giab057","DOI":"10.1093\/gigascience\/giab057","article-title":"VC@Scale: Scalable and High-Performance Variant Calling on Cluster Environments","volume":"10","author":"Ahmad","year":"2021","journal-title":"GigaScience"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1768","DOI":"10.1093\/bioinformatics\/bty894","article-title":"VCPA: Genomic Variant Calling Pipeline and Data Management Tool for Alzheimer\u2019s Disease Sequencing Project","volume":"35","author":"Leung","year":"2019","journal-title":"Bioinformatics"},{"doi-asserted-by":"crossref","unstructured":"Chiara, M., Gioiosa, S., Chillemi, G., D\u2019Antonio, M., Flati, T., Picardi, E., Zambelli, F., Horner, D.S., Pesole, G., and Castrignan\u00f2, T. (2018). CoVaCS: A Consensus Variant Calling System. BMC Genom., 19.","key":"ref_35","DOI":"10.1186\/s12864-018-4508-1"},{"doi-asserted-by":"crossref","unstructured":"Reid, J.G., Carroll, A., Veeraraghavan, N., Dahdouli, M., Sundquist, A., English, A., Bainbridge, M., White, S., Salerno, W., and Buhay, C. (2014). Launching Genomics into the Cloud: Deployment of Mercury, a next Generation Sequence Analysis Pipeline. BMC Bioinform., 15.","key":"ref_36","DOI":"10.1186\/1471-2105-15-30"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1093\/gbe\/evw041","article-title":"Whole Genome Identification, Phylogeny and Evolution of the Cytochrome P450 Family 2 (CYP2) Sub-Families in Birds","volume":"8","author":"Almeida","year":"2016","journal-title":"Genome Biol. Evol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2832","DOI":"10.1093\/molbev\/msv155","article-title":"Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida","volume":"32","author":"Khan","year":"2015","journal-title":"Mol. Biol. Evol."},{"doi-asserted-by":"crossref","unstructured":"Alvelos, M.I., Gon\u00e7alves, C.I., Coutinho, E., Almeida, J.T., Bastos, M., Sampaio, M.L., Melo, M., Martins, S., Dinis, I., and Mirante, A. (2020). Maturity-Onset Diabetes of the Young (MODY) in Portugal: Novel GCK, HNFA1 and HNFA4 Mutations. J. Clin. Med., 9.","key":"ref_39","DOI":"10.3390\/jcm9010288"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1002\/humu.24052","article-title":"Hypoparathyroidism, Deafness, and Renal Dysplasia Syndrome: 20 Years after the Identification of the First GATA3 Mutations","volume":"41","author":"Lemos","year":"2020","journal-title":"Hum. Mutat."},{"doi-asserted-by":"crossref","unstructured":"Maldonado, E., and Khan, I. (2024). Omics Biology in Diagnosis of Diseases: Towards Empowering Genomic Medicine from an Evolutionary Perspective. Life, 14.","key":"ref_41","DOI":"10.3390\/life14121637"},{"unstructured":"Maldonado, E., and Khan, I. (2025). Multi-Omics for Diagnosing Diseases: Bioinformatics Approaches and Integrative Data Analyses. Computation, Available online: https:\/\/www.mdpi.com\/journal\/computation\/special_issues\/D97DPHGA83.","key":"ref_42"},{"unstructured":"Maldonado, E., and Khan, I. (2025). Multi-Omics for Diagnosing Diseases: Bioinformatics Approaches and Integrative Data Analyses. Life, Available online: https:\/\/www.mdpi.com\/journal\/life\/special_issues\/15JSWLKS45.","key":"ref_43"},{"doi-asserted-by":"crossref","unstructured":"Fernandes, M.Z., Caetano, C.F., Gaspar, C., Oliveira, A.S., Palmeira-de-Oliveira, R., Martinez-de-Oliveira, J., Rolo, J., and Palmeira-de-Oliveira, A. (2023). Uncovering the Yeast Diversity in the Female Genital Tract: An Exploration of Spatial Distribution and Antifungal Resistance. Pathogens, 12.","key":"ref_44","DOI":"10.3390\/pathogens12040595"},{"doi-asserted-by":"crossref","unstructured":"Caetano, C.F., Gaspar, C., Oliveira, A.S., Palmeira-de-Oliveira, R., Rodrigues, L., Gon\u00e7alves, T., Martinez-de-Oliveira, J., Palmeira-de-Oliveira, A., and Rolo, J. (2023). Study of Ecological Relationship of Yeast Species with Candida Albicans in the Context of Vulvovaginal Infections. Microorganisms, 11.","key":"ref_45","DOI":"10.3390\/microorganisms11102398"},{"doi-asserted-by":"crossref","unstructured":"Bonif\u00e1cio, M., Mateus, C., Alves, A.R., Maldonado, E., Duarte, A.P., Domingues, F., Oleastro, M., and Ferreira, S. (2021). Natural Transformation as a Mechanism of Horizontal Gene Transfer in Aliarcobacter Butzleri. Pathogens, 10.","key":"ref_46","DOI":"10.3390\/pathogens10070909"},{"unstructured":"(2024, June 13). University of Beira Interior C4-UBI\u2014Cloud Computing Competence Centre, University of Beira Interior. Available online: https:\/\/c4.ubi.pt\/.","key":"ref_47"},{"key":"ref_48","first-page":"e000086","article-title":"CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): An Online Resource for the Medical Microbiology Community","volume":"2","author":"Connor","year":"2016","journal-title":"Microb. Genom."},{"doi-asserted-by":"crossref","unstructured":"Bagheri, H., Muppirala, U., Masonbrink, R.E., Severin, A.J., and Rajan, H. (2019). Shared Data Science Infrastructure for Genomics Data. BMC Bioinform., 20.","key":"ref_49","DOI":"10.1186\/s12859-019-2967-2"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"baw022","DOI":"10.1093\/database\/baw022","article-title":"High-Performance Integrated Virtual Environment (HIVE): A Robust Infrastructure for next-Generation Sequence Data Analysis","volume":"2016","author":"Simonyan","year":"2016","journal-title":"Database"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e26681","DOI":"10.2196\/26681","article-title":"Design and Implementation of an Informatics Infrastructure for Standardized Data Acquisition, Transfer, Storage, and Export in Psychiatric Clinical Routine: Feasibility Study","volume":"8","author":"Blitz","year":"2021","journal-title":"JMIR Ment. Health"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1136\/jamia.2001.0080199","article-title":"An Informatics Infrastructure Is Essential for Evidence-Based Practice","volume":"8","author":"Bakken","year":"2001","journal-title":"J. Am. Med. Inform. Assoc."},{"doi-asserted-by":"crossref","unstructured":"Forghani, A., Sadjadi, S.J., and Moghadam, B.F. (2018). A Supplier Selection Model in Pharmaceutical Supply Chain Using PCA, Z-TOPSIS and MILP: A Case Study. PLoS ONE, 13.","key":"ref_53","DOI":"10.1371\/journal.pone.0201604"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1016\/j.compind.2010.12.001","article-title":"Power-Based Supplier Selection in Product Development Projects","volume":"62","author":"Zolghadri","year":"2011","journal-title":"Comput. Ind."},{"unstructured":"Schrader, D. (2024, March 10). The Fundamentals of Network Access Management. Available online: https:\/\/blog.netwrix.com\/.","key":"ref_55"},{"unstructured":"Gubin, A.V. (2023, August 07). ZFS RAIDZ vs. Traditional RAID. Available online: https:\/\/www.klennet.com\/notes\/2019-07-04-raid5-vs-raidz.aspx.","key":"ref_56"},{"doi-asserted-by":"crossref","unstructured":"Patterson, D.A., Gibson, G., and Katz, R.H. (1988, January 1\u20133). A Case for Redundant Arrays of Inexpensive Disks (RAID). Proceedings of the 1988 ACM SIGMOD International Conference on Management of Data, Chicago, IL, USA.","key":"ref_57","DOI":"10.1145\/50202.50214"},{"unstructured":"(2024, June 13). iXsystems TrueNAS SCALE\u2014Linux-Based Open Source Storage Infrastructure. Available online: https:\/\/www.truenas.com\/truenas-scale\/.","key":"ref_58"},{"unstructured":"Salter, J. (2023, August 07). ZFS Fans, Rejoice\u2014RAIDz Expansion Will Be a Thing Very Soon. Available online: https:\/\/arstechnica.com\/gadgets\/2021\/06\/raidz-expansion-code-lands-in-openzfs-master\/.","key":"ref_59"},{"unstructured":"(2023, August 07). Calomel.org ZFS Raidz Performance, Capacity and Integrity Comparison @ Calomel.Org. Available online: https:\/\/calomel.org\/zfs_raid_speed_capacity.html.","key":"ref_60"},{"doi-asserted-by":"crossref","unstructured":"Qiao, Z., Fu, S., Chen, H.-B., and Settlemyer, B. (2019, January 23\u201326). Building Reliable High-Performance Storage Systems: An Empirical and Analytical Study. Proceedings of the 2019 IEEE International Conference on Cluster Computing (CLUSTER), Albuquerque, Mexico.","key":"ref_61","DOI":"10.1109\/CLUSTER.2019.8891006"},{"doi-asserted-by":"crossref","unstructured":"Qiao, Z., Liang, S., Fu, S., Chen, H.-B., and Settlemyer, B. (2019, January 24\u201327). Characterizing and Modeling Reliability of Declustered RAID for HPC Storage Systems. Proceedings of the 2019 49th Annual IEEE\/IFIP International Conference on Dependable Systems and Networks\u2014Industry Track, Portland, OR, USA.","key":"ref_62","DOI":"10.1109\/DSN-Industry.2019.00011"},{"unstructured":"(2023, August 07). OpenZFS dRAID\u2014OpenZFS Documentation. Available online: https:\/\/openzfs.github.io\/openzfs-docs\/Basic%20Concepts\/dRAID%20Howto.html.","key":"ref_63"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1145\/143371.143383","article-title":"Parity Declustering for Continuous Operation in Redundant Disk Arrays","volume":"27","author":"Holland","year":"1992","journal-title":"ACM SIGPLAN Not."},{"unstructured":"(2024, June 14). iXsystems ZFS Primer. Available online: https:\/\/www.truenas.com\/docs\/references\/zfsprimer\/.","key":"ref_65"},{"unstructured":"Infostor (2024, June 13). LinuxCon: OpenZFS Moves Open Source Storage Forward\u2014Infostor.com\u00ae. Infostor.com. Available online: https:\/\/www.infostor.com\/storage-management\/linuxcon-openzfs-moves-open-source-storage-forward.html.","key":"ref_66"},{"unstructured":"(2023, August 07). iXsystems SCALE Hardware Guide. Available online: https:\/\/www.truenas.com\/docs\/scale\/gettingstarted\/scalehardwareguide\/.","key":"ref_67"},{"unstructured":"Harris, R. (2023, August 07). Why RAID 5 Stops Working in 2009. Available online: https:\/\/www.zdnet.com\/article\/why-raid-5-stops-working-in-2009\/.","key":"ref_68"},{"unstructured":"Harris, R. (2023, August 07). Why RAID 6 Stops Working in 2019. Available online: https:\/\/www.zdnet.com\/article\/why-raid-6-stops-working-in-2019\/.","key":"ref_69"},{"unstructured":"(2023, August 07). iXsystems TrueNAS Community. Available online: https:\/\/www.truenas.com\/community\/.","key":"ref_70"},{"unstructured":"(2024, June 13). iXsystems ZFS dRAID Primer. Available online: https:\/\/www.truenas.com\/docs\/references\/draidprimer\/.","key":"ref_71"},{"unstructured":"(2023, August 07). IDEMA The Advent of Advanced Format | IDEMA. Available online: https:\/\/idema.org\/?page_id=2369.","key":"ref_72"},{"unstructured":"Fitzpatrick, M.E. (2011). 4K Sector Disk Drives: Transitioning to the Future with Advanced Format Technologies, Toshiba America Information Systems, Inc.","key":"ref_73"},{"unstructured":"(2023, August 07). Seagate Transition to Advanced Format 4K Sector Hard Drives | Seagate US. Available online: https:\/\/www.seagate.com\/blog\/advanced-format-4k-sector-hard-drives-master-ti\/.","key":"ref_74"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s44342-024-00032-1","article-title":"Rare Disease Genomics and Precision Medicine","volume":"22","author":"Hong","year":"2024","journal-title":"Genom. Inform."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"103953","DOI":"10.1016\/j.ijmedinf.2019.103953","article-title":"Legal Framework for Health Cloud: A Systematic Review","volume":"132","author":"Zandesh","year":"2019","journal-title":"Int. J. Med. Inf."},{"doi-asserted-by":"crossref","unstructured":"Hekel, R., Budis, J., Kucharik, M., Radvanszky, J., P\u00f6s, Z., and Szemes, T. (2021). Privacy-Preserving Storage of Sequenced Genomic Data. BMC Genom., 22.","key":"ref_77","DOI":"10.1186\/s12864-021-07996-2"},{"unstructured":"Cabading, Z. (2023, August 07). SAS vs SATA: What\u2019s the Difference? | HP\u00ae Tech Takes. Available online: https:\/\/www.hp.com\/us-en\/shop\/tech-takes\/sas-vs-sata.","key":"ref_78"},{"unstructured":"Cook, J.D. (2023, August 07). Hard Disk Array Failure Probabilities. Available online: https:\/\/www.johndcook.com\/blog\/2009\/01\/05\/rai-failure-probabilities\/.","key":"ref_79"},{"doi-asserted-by":"crossref","unstructured":"Wood, D.E., Lu, J., and Langmead, B. (2019). Improved Metagenomic Analysis with Kraken 2. Genome Biol., 20.","key":"ref_80","DOI":"10.1186\/s13059-019-1891-0"},{"doi-asserted-by":"crossref","unstructured":"Wood, D.E., and Salzberg, S.L. (2014). Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments. Genome Biol., 15.","key":"ref_81","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1093\/molbev\/msp259","article-title":"SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building","volume":"27","author":"Gouy","year":"2010","journal-title":"Mol. Biol. Evol."},{"unstructured":"Katoh, K. (2021). Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation. Multiple Sequence Alignment: Methods and Protocols, Springer.","key":"ref_83"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative Genomics Viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","article-title":"Predicting Splicing from Primary Sequence with Deep Learning","volume":"176","author":"Jaganathan","year":"2019","journal-title":"Cell"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: Phylogenetic Analysis by Maximum Likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. Biol."},{"doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and Applications. BMC Bioinform., 10.","key":"ref_88","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences","volume":"15","author":"Dale","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map Format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","article-title":"BamTools: A C++ API and Toolkit for Analyzing and Managing BAM Files","volume":"27","author":"Barnett","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkab1053","article-title":"The Sequence Read Archive: A Decade More of Explosive Growth","volume":"50","author":"Katz","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"giad067","DOI":"10.1093\/gigascience\/giad067","article-title":"ARA: A Flexible Pipeline for Automated Exploration of NCBI SRA Datasets","volume":"12","author":"Maurya","year":"2023","journal-title":"GigaScience"},{"unstructured":"Andrews, S. (2025, February 13). FastQC A Quality Control Tool for High Throughput Sequence Data. Available online: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/.","key":"ref_94"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies","volume":"27","author":"Salzberg","year":"2011","journal-title":"Bioinformatics"},{"unstructured":"Krueger, F. (2025, February 13). Trim Galore!: A Wrapper around Cutadapt and FastQC to Consistently Apply Adapter and Quality Trimming to FastQ Files, with Extra Functionality for RRBS Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/.","key":"ref_96"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality Assessment Tool for Genome Assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs","volume":"31","author":"Waterhouse","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"i302","DOI":"10.1093\/bioinformatics\/btu280","article-title":"Ragout\u2014A Reference-Assisted Assembly Tool for Bacterial Genomes","volume":"30","author":"Kolmogorov","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_101","first-page":"e18","article-title":"NOVOPlasty: De Novo Assembly of Organelle Genomes from Whole Genome Data","volume":"45","author":"Dierckxsens","year":"2017","journal-title":"Nucleic Acids Res."},{"doi-asserted-by":"crossref","unstructured":"Boras, M., Balen, J., and Vdovjak, K. (2020, January 14\u201316). Performance Evaluation of Linux Operating Systems. Proceedings of the 2020 International Conference on Smart Systems and Technologies (SST), Osijek, Croatia.","key":"ref_102","DOI":"10.1109\/SST49455.2020.9264055"},{"key":"ref_103","first-page":"343","article-title":"Comparative Performance Evaluation of Popular Virtual Private Servers","volume":"21","author":"Balen","year":"2020","journal-title":"J. Internet Technol."},{"unstructured":"(2024, August 27). CPUID POWERMAX | Softwares | CPUID. Available online: https:\/\/www.cpuid.com\/softwares\/powermax.html.","key":"ref_104"},{"unstructured":"(2024, August 27). CPUID CPU-Z | Softwares | CPUID. Available online: https:\/\/www.cpuid.com\/softwares\/cpu-z.html.","key":"ref_105"},{"unstructured":"Miyazaki, N. (2024, August 27). CrystalDiskMark. Available online: https:\/\/sourceforge.net\/projects\/crystaldiskmark\/.","key":"ref_106"},{"unstructured":"(2024, August 27). Phoronix Media Phoronix Test Suite\u2014Linux Testing & Benchmarking Platform, Automated Testing, Open-Source Benchmarking. Available online: https:\/\/www.phoronix-test-suite.com\/.","key":"ref_107"},{"unstructured":"Primate Labs Inc (2024, August 27). Geekbench 6\u2014Cross-Platform Benchmark. Available online: https:\/\/www.geekbench.com\/.","key":"ref_108"},{"unstructured":"(2024, August 27). Ultimate Systems HARDiNFO Benchmark\u2014The Ultimate Hardware Performance Benchmarks. Available online: https:\/\/www.hardinfo-benchmark.com\/.","key":"ref_109"},{"unstructured":"Dugan, J., Elliott, S., Mah, B.A., Poskanzer, J., Prabhu, K., Ashley, M., Brown, A., Jai\u00dfle, A., Sahani, S., and Simpson, B. (2024, August 27). iPerf\u2014The TCP, UDP and SCTP Network Bandwidth Measurement Tool. Available online: https:\/\/iperf.fr\/.","key":"ref_110"},{"unstructured":"Lucas, K. (2024, August 27). Kdlucas\/Byte-Unixbench\u2014A Unix Benchmark Suite. Available online: https:\/\/github.com\/kdlucas\/byte-unixbench.","key":"ref_111"}],"container-title":["Technologies"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2227-7080\/13\/7\/285\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:04:21Z","timestamp":1760033061000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2227-7080\/13\/7\/285"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,4]]},"references-count":111,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["technologies13070285"],"URL":"https:\/\/doi.org\/10.3390\/technologies13070285","relation":{},"ISSN":["2227-7080"],"issn-type":[{"type":"electronic","value":"2227-7080"}],"subject":[],"published":{"date-parts":[[2025,7,4]]}}}