Evaluated articles

A list by GigaByte

Articles that have been evaluated by GigaByte.

102 articlesLast updated

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  1. Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo

    1. Victoire Nsabatien
    2. Josue Zanga
    3. Fiacre Agossa
    4. Nono Mvuama
    5. Maxwell Bamba
    6. Osée Mansiangi
    7. Leon Mbashi
    8. Vanessa Mvudi
    9. Glodie Diza
    10. Dorcas Kantin
    11. Narcisse Basosila
    12. Hyacinthe Lukoki
    13. Arsene Bokulu
    14. Christelle Bosulu
    15. Erick Bukaka
    16. Jonas Nagahuedi
    17. Jean Claude Palata
    18. Emery Metelo

    • Curated by GigaByte

      Editors Assessment: Aedes mosquito spread Arbovirus epidemics (e.g. Chikungunya, dengue, West Nile, Yellow Fever, and Zika), are a growing threat in Africa but a lack of vector data limits our ability to understand their propagation dynamics. This work describes the geographical distribution of Ae. aegypti and Ae. albopictus in Kinshasa, Democratic Republic of Congo between 2020 and 2022. Sharing 6,943 observations under a CC0 waiver as a Darwin Core archive in the University of Kinshasa GBIF database. Review improved the metadata by adding more accurate date information, and this data can provide important information for further basic and advanced studies on the ecology and phenology of these vectors in West Africa.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    2 evaluationsAppears in 2 listsLatest version Latest activity

  2. A reference assembly for the legume cover crop hairy vetch (Vicia villosa)

    1. Tyson Fuller
    2. Derek M. Bickhart
    3. Lisa M. Koch
    4. Lisa Kissing Kucek
    5. Shahjahan Ali
    6. Haley Mangelson
    7. Maria J. Monteros
    8. Timothy Hernandez
    9. Timothy P. L. Smith
    10. Heathcliffe Riday
    11. Michael L. Sullivan

    • Curated by GigaByte

      Editors Assessment:

      The hairy vetch Vicia villosa is an annual legume widely used as a cover crop due to its ability to withstand harsh winters. Here a new a 2.03GB reference-quality genome is presented, assembled from PacBio HiFi long-sequence reads and Hi-C scaffolding. After adding some more methodological details and long-terminal repeat (LTR) assembly index (LAI) analysis the assembly quality and metrics look quite convincing as a chromosome-scale assembly. This resource hopefully providing the foundation for a genetic improvement program for this important cover crop and forage species.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    2 evaluationsAppears in 2 listsLatest version Latest activity

  3. Genome assembly of the bearded iris Iris pallida Lam

    1. Robert E. Bruccoleri
    2. Edward J. Oakeley
    3. Ann Marie E Faust
    4. Marc Altorfer
    5. Sophie Dessus-Babus
    6. David Burckhardt
    7. Mevion Oertli
    8. Ulrike Naumann
    9. Frank Petersen
    10. Joanne Wong

    • Curated by GigaByte

      **Editors Assessment: **

      Irises on top of being a popular and beautiful ornamental plant, have wider commercial interest due to the many interesting secondary metabolites present in their rhizomes that have value to the fragrance and pharmaceutical industries. Many of these have large and difficult to assemble genomes, and to fill that gap the Dalmatian Iris (Iris pallida Lam.) is sequenced here. Using PacBio long-read sequencing and bionano optical mapping to produce a giant 10Gbp assembly with a scaffold N50 of 14.34 Mbp. The authors didn’t manage to handle the haplotigs separately or to study the ploidy, but as all of the data is available for reuse others can explore these questions further. This reference genome should also allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    2 evaluationsAppears in 2 listsLatest version Latest activity

  4. A Database of Restriction Maps to Expand the Utility of Bacterial Artificial Chromosomes

    1. Eamon Winden
    2. Alejandro Vasquez-Echeverri
    3. Susana Calle-Casteneda
    4. Yumin Lian
    5. Juan Pablo Hernández-Ortiz
    6. David C. Schwartz

    • Curated by GigaByte

      **Editors Assessment: **

      While Bacterial Artificial Chromosomes libraries were once a key resource for building the human genome project over time they have been rendered relatively obsolete by long-read technologies. In the era of CRISPR-Cas systems pairing this data with one of the many guide-RNA libraries to find targets for manipulation with CRISPR tools is bringing back BACs advantages for genomics. With this in mind the authors have developed a BAC restriction map database containing the restriction maps for both uniquely placed and insert-sequenced BACs from 11 libraries covering the recognition sequences of available restriction enzymes. Alongside a set of Python functions to reconstruct the database and more easily access it (which were debugged and had improved documentation added during review). The presented data should be valuable for researchers simply using BACs, as well as those working with larger sections of the genome in terms of synthetic genes, large-scale editing, and mapping.

      *This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    3 evaluationsAppears in 2 listsLatest version Latest activity

  5. Trumpet plots: Visualizing The Relationship Between Allele Frequency And Effect Size In Genetic Association Studies

    1. Lucia Corte
    2. Lathan Liou
    3. Paul F. O’Reilly
    4. Judit García-González

    • Curated by GigaByte

      **Editors Assessment: **

      This work presents a new standardized graphical approach for visualizing genetic associations across a wide range of allele frequencies. These proposed TrumpetPlots have a distinctive trumpet shape, hence the proposed name. With the majority of variants having low frequency and small effects, while a small number of variants have higher frequency and larger effects, this view can help to provide new and valuable insights into the genetic basis of traits and diseases, and also help prioritize efforts to discover new risk variants. The tool is provided as a novel R package and R Shiny application and to demonstrate its use the article illustrates the distribution of variant effect sizes across the allele frequency range for over 100 continuous traits available in the UK Biobank. After some problems in testing the package is now available and easy to deploy via CRAN.

      *This assessment refers to version 1 of this preprint. *

    Reviewed by GigaByte

    3 evaluationsAppears in 2 listsLatest version Latest activity

  6. Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

    1. Sagar Patel
    2. Zachary N. Harris
    3. Jason P. Londo
    4. Allison Miller
    5. Anne Fennell

    • Curated by GigaByte

      Editor’s Assessment

      Hybrid genomes are tricky to assemble, and few genomic resources are available for hybrid grapevines such as ‘Chambourcin’, a French-American interspecific hybrid grape grown in the eastern and midwestern United States. Here is an attempt to assemble Chambourcin’ using a combination of PacBio HiFi long-reads, Bionano optical maps, and Illumina short-read sequencing technologies. Producing an assembly with 26 scaffolds, an N50 length 23.3 Mb and an estimated BUSCO completeness of 97.9% that can be used for genome comparisons, functional genomic analyses, and genome-assisted breeding research. Error correction and pilon polishing was a challenge with this hybrid assembly, but after trying a few different approaches in the review process have improved it, and as they have documented what they did and are clear about the final metrics, users can assess the quality themselves.

      This assessment refers to version 2 of this preprint.

    Reviewed by GigaByte

    2 evaluationsAppears in 4 listsLatest version Latest activity

  7. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

    1. André Gomes-dos-Santos
    2. Manuel Lopes-Lima
    3. André M. Machado
    4. Thomas Forest
    5. Guillaume Achaz
    6. Amílcar Teixeira
    7. Vincent Prié
    8. L. Filipe C. Castro
    9. Elsa Froufe

    • Curated by GigaByte

      Editor’s Assessment

      Like other mollusc species, the freshwater pearl mussel (Margaritifera margaritifera) has a challenging genome to assemble owing to the large size of their genomes, heterozygosity, and repetitive sequence. The first published M. margaritifera genome was highly fragmented, but here an improved reference genome assembly was generated using PacBio CLR long reads to reduce fragmentation levels, missing and truncated genes, and chimerically assembled regions. The number of gene models predicted is a bit higher compared than other molluscan genomes, but after clarification and double checking these seem in line with some Mollusca and Bivalvia with similar and higher numbers of gene predictions. This new genome represents a new resource to start exploring the many biological, ecological, and evolutionary features of this threatened and commercially important group of organisms.

      This assessment refers to version 1 of this preprint.

    Reviewed by GigaByte

    2 evaluationsAppears in 2 listsLatest version Latest activity

  8. Mycobacterial Metabolic Model Development for Drug Target Identification

    1. Bridget P. Bannerman
    2. Alex Oarga
    3. Jorge Júlvez

    • Curated by GigaByte

      Editor’s Assessment

      This work has generated metabolic models for the human pathogens Mycobacterium leprae and Mycobacteroides abscessus, alongside a new computational tool that can be used to identify potential drug targets. The standardised genomic scale metabolic models have been developed using the systems biology community standards for quality control and evaluation of models. After providing more detail on reproducibility, comparative performance of the models, and reuse, these resources are now published and are available for reuse by the global scientific community via the GigaDB, Biomodels, and PatMeDB repositories.

      This assessment refers to version 1 of this preprint.

    Reviewed by GigaByte

    2 evaluationsAppears in 2 listsLatest version Latest activity

  16. A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

    1. Nataly Allasi Canales
    2. Oscar A. Pérez-Escobar
    3. Robyn F. Powell
    4. Mats Töpel
    5. Catherine Kidner
    6. Mark Nesbitt
    7. Carla Maldonado
    8. Christopher J. Barnes
    9. Nina Rønsted
    10. Natalia A. S. Przelomska
    11. Ilia J. Leitch
    12. Alexandre Antonelli

    Reviewed by GigaByte

    1 evaluationAppears in 1 listLatest version Latest activity
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