DeNovo approaches

Biotechvana is glad to offer data analysis services for different approaches “de novo” including assembly and annotation of both prokaryotic and eukaryotic genomes and transcriptomes without available reference, as well as WGS Metagenomics and Metatranscriptomics.

We also offer services for viruses and mobile elements full-length genome characterization or exhaustive characterization of the complete population of mobile genetic elements or viruses (mobilome or viriome) of a host or a sample. Although each study needs to be personalized depending on your experiment and the species to be characterized below we summarize the usual workflow followed by us in these types of studies.

Genomes, Transcriptomes, Metagenomes, Metatranscriptomes

1) Preprocessing of raw data 2) De Novo Assembly and scaffolding 3) Annotation and functional analysis 4) Downstream analyses

Full-length Genome Characterization of Virus and Mobile Genetic Elements

1) Preprocessing of raw data 2) De Novo Assembly 3) Annotation

Viriome/Mobilome annotation

1) Mapping and Annotation 2) Integration and downstream analyses

If you are interested in getting more information about our services for analysis of DeNovoSeq data, please contact us at biotechvana(at) and we will be glad to pass you on a quote or organize a personalized meeting with you in order to discuss and evaluate your experiment.

Related publications

  • Hafez A and 17 co-authors (including Soriano B, Ceprian R, Elsayed. AA, MArtinez G, and llorens C). 2022. RNASeq and VariantSeq applications and Server Side of GPRO suite. ArXiv
  • Navarrete-Muñoz MA, Llorens C, Benito JM, Rallon N. 2022. Extracellular Vesicles as a New Promising Therapy in HIV Infection. Front. Immunol., 04 January 2022.
  • Soriano B, Kuprovic M, Llorens C. ICTV Report Consortium. 2021. ICTV Virus Taxonomy Profile: Belpaoviridae 2021.Journal of General Virology,102-11.
  • Arcos SC (and 14 coauthors including Llorens C). 2021.Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae. Microorganisms 9(5):1088.doi:
  • Llorens C, Soriano B, Navarrete-Muñoz MA, Hafez A, Arnau V, Benito JM, Gabaldon T, Rallon N, Perez-Sanchez J, Kropovic M. 2021. Reverse-transcribing viruses of the families Metaviridae, Belpaoviridae and Pseudoviridae (order Ortervirales). In: Bamford, D.H. and Zuckerman, M. (eds.) Encyclopedia of Virology, 4th Edition, vol. 3, pp. 653-666. Oxford: Academic Press. Elsevier, doi:
  • Pérez-Sánchez R, Carnero-Morán Á, Soriano B, Llorens C, Oleaga A. 2021. RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle. Parasites Vectors 14, 170.
  • Oleaga A, Soriano B, Llorens C, Pérez-Sánchez R. 2021. Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle. PLOS Neglected Tropical Diseases 15(2): e0009105.
  • Llorens C, Soriano B, Kuprovic M, ICTV Report Consortium. 2021. ICTV Virus Taxonomy Profile: Pseudoviridae. Journal of General Virology,102-3
  • Llorens C, Soriano B, Kuprovic M, ICTV Report Consortium. 2020.ICTV Virus Taxonomy Profile: Metaviridae. Journal of General Virology, 101-11
  • Trilla-Fuertes L, Ramos-Ruiz R, Blanca-Lopez N, Lopez-Camacho E, Martin-Pedraza L, Ryan Murua P, Diaz-Almiron M, Llorens C, Gabaldon T, Moya A, Fresno JA, Gamez-Pozo A. 2020. Functional characterization of SARS-CoV-2 infection suggests a complex inflammatory response and metabolic alterations. BioRxiv
  • Pérez-Sánchez J, Naya-Català F, Soriano B, Piazzon MA, Hafez A, Gabaldón T, Llorens C, Sitjà-Bobadilla A, Calduch-Giner J. 2019. Genome Sequencing and Transcriptome Analysis Reveal Recent Species-specific Gene Duplications in the Plastic Gilthead Sea Bream. Front. Mar. Sci. 20
  • Rodríguez-García E, Olagüe C, Ríus-Rocabert S, Ferrero R, Llorens C, Larrea E, Fortes P, Prieto J, González-Aseguinolaza G, Nistal-Villan E.2018 TMEM173 Alternative Spliced Isoforms Modulate Viral Replication through the STING Pathway. ImmunoHorizons, 2,11 pp 363-376.
  • Garcia-Jimenez P, Llorens C, Roig FJ, Robina RR.2018 Analysis of the Transcriptome of the Red Seaweed Grateloupia imbricata with Emphasis on Reproductive Potential. Marine Drugs, 16,490.
  • Llorens C, Arcos SC, Robertson L, Ramos R, Futami R, Soriano B, Ciordia S, Careche M, González-Muñoz M, Jiménez-Ruiz Y, Carballeda-Sangiao N, Moneo I, Albar JP, Blaxter M and Navas A. 2018.Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns. BMC Genomics 19:592.
  • Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski N, Pappu HR, Pooggin M, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon S, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH. 2018. Ortervirales: A new viral order unifying five families of reverse-transcribing viruses. Journal of Virology. 92:12 5 e00515-18
  • Roig F, Gonzalez-Candelas F, Sanjuan E, Feil E, Fouz B, Llorens C, Baker-Austin C, Oliver J, Danin-Poleg Y, Gibas C, Kashi Y, Gulig PA, Morrison SS, Amaro C. 2018. Phylogeny of Vibrio vulnificus from the analysis of the core-genome: implications for intra-species taxonomy. Front. Microbiol. 8, 2613; doi: 10.3389/fmicb.2017.02613
  • Unver T, Wu Z, Sterck L, Turktas M, Lohaus R, Li Z, Yang M, He L, Deng T, Escalante FJ, Llorens C, Roig FJ, Parmaksiz I, Dundar E, Xie F, Zhang B, Ipek A, Uranbey S, Erayman M, Ilhan E, Badad O, Ghazal H, Lightfoot DA, Kasarla P, Colantonio V, Tombologlu H, Hernandez P, Mete N, Cetin O, Van Montagu M, Yang H, Gao Q, Dorado G, and Van de Peer Y. 2017. Genome of wild olive and the evolution of oil biosynthesis Proc. Natl. Acad. Sci. USA. 2017, 114, 44: E9413-E9422, doi:10.1073/pnas.1708621114.
  • Ramirez M, Velázquez R, López-Piñeiro A, Naranjo B, Roig F and Llorens C. 2017. New Insights into the Genome Organization of Yeast Killer Viruses Based on “Atypical” Killer Strains Characterized by High-Throughput Sequencing. Toxins 9(9), 292; doi:10.3390/toxins9090292
  • Lysøe E, Harris LJ, Walkowiak S, Subramaniam R, Divon HH, Riiser ES, Llorens C, Gabaldón T, Kistler HH, Jonkers W, Kolseth AK, Nielsen KF, Thrane U, and Frandsen RJN. 2014. The Genome of the Generalist Plant Pathogen Fusarium avenaceum Is Enriched with Genes Involved in Redox, Signaling and Secondary Metabolism. PLoS ONE 9(11): e112703. doi:10.1371/journal.pone.0112703
  • Carmona bayonas A, Luengo Gil G, Fong Puig CA, Llorens C. 2013. Los elementos geneticos moviles en la celula tumoral: El despertar de un gigante. REVISTA EUBACTERIA (NOVIEMBRE 2013) Nº32 / ISSN-1697-0071
  • Llorens C, Bernet GP, Ramasamy S, Feschotte C, Moya A 2012. On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. Mobile Genetic Elements 2(5), September-October-2012.
  • Bernet GP, Muñoz-Pomer A, Dominguez-Escriba L, Covelli L, Bernad L, Ramasamy S, Futami R, Sempere JM, Moya A and Llorens C. 2011. GyDB Mobilomics: LTR retroelements and integrase-related transposons of the Pea aphid Acyrthosiphon pisum genome. Mobile Genetic Elements 1(2), 0-1. 1-7-2011. Landes Bioscience.
  • Covelli L, Muñoz-Pomer A, Dominguez-Escriba L, Futami R, Bernet GP, Moya A and Llorens C. 2011. The GyDB collection is now publicly available within the Gypsy Database of Mobile Genetic Elements. Biotechvana bioinformatics:2011-CR1
  • Llorens C, Futami R, Covelli L, Dominguez-Escriba L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, and Moya A. 2011. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061
  • THE INTERNATIONAL APHID GENOMICS CONSORTIUM (including Llorens C and Futami R). 2010 . Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol, 8(2):e1000313 DOI / ISBN:10.1371/journal.pbio.1000313
  • Llorens C, Muñoz-Pomer A, Bernad L, Botella H, and Moya A. 2009. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biology Direct, 4:41
  • Llorens C, Muñoz-Pomer A, Futami R, and Moya A. 2009. The GyDB Collection of Viral and Mobile Genetic Element Models. In Biotechvana Bioinformatics, CR: GyDB collection V2
  • Llorens C, Fares MA, and Moya A. 2008. Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. BMC Evolutionary Biology, 8:276
  • Llorens C, Futami R, Bezemer D and Moya A. 2008. The Gypsy Database (GyDB) of mobile genetic elements. Nucleic Acids Research (NAR) 36 (Database Issue):38-46
  • Llorens C and Marin I. 2001. A mammalian gene evolved from the Integrase domain of an LTR-retrotransposon. Molecular Biology and Evolution. 18 (8): 1597-1600
  • Marin I and Llorens C. 2000. "Ty3/Gypsy Retrotransposons: Description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data". Molecular Biology and Evolution. 17(7): 1040-1049

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    Hipra Scientific S.L.U, Polypeptide Therapeutic Solutions S.L., Biotechvana S.L. and Nostrum Biodiscovery constitute the consortium of enterprises participating in the project "Research of a new vaccine for a human respiratory disease", granted by the CDTI (Center for Industrial Technological Development), and supported by the Ministry of Science and Innovation and financed by the European Union – NextGenerationEU. The main objective of this project is to design a safe immunogenic and effective vaccine against the respiratory syncytial virus.

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