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  1. SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics

    This article has 17 authors:
    1. Chun Gong
    2. Shengkang Li
    3. Leying Wang
    4. Fuxiang Zhao
    5. Shuangsang Fang
    6. Dong Yuan
    7. Zijian Zhao
    8. Qiqi He
    9. Mei Li
    10. Weiqing Liu
    11. Zhaoxun Li
    12. Hongqing Xie
    13. Sha Liao
    14. Ao Chen
    15. Yong Zhang
    16. Yuxiang Li
    17. Xun Xu
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      One limiting factor in the adoption of spatial omics research are workflow systems for data preprocessing, and to address these authors developed the SAW tool to process Stereo-seq data. The analysis steps of spatial transcriptomics involve obtaining gene expression information from space and cells. Existing tools face issues with large data sets, such as intensive spatial localization, RNA alignment, and excessive memory usage. These issues affect the process's applicability and efficiency. To address this, this paper presents a high-performance open-source workflow called SAW for Stereo-Seq. This includes mRNA position reconstruction, genome alignment, matrix generation, clustering, and result file generation for personalized analysis. During review the authors have added examples of MID correction in the article to make the process easier to understand. And In the future, more accurate algorithms or deep learning models may further improve the accuracy of this pipeline.

      *This evaluation refers to version 1 of the preprint

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  2. Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images

    This article has 14 authors:
    1. Bohan Zhang
    2. Mei Li
    3. Qiang Kang
    4. Zhonghan Deng
    5. Hua Qin
    6. Kui Su
    7. Xiuwen Feng
    8. Lichuan Chen
    9. Huanlin Liu
    10. Shuangsang Fang
    11. Yong Zhang
    12. Yuxiang Li
    13. Susanne Brix
    14. Xun Xu
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      This paper describes a new spatial transcriptomics method that that utilizes cell nuclei staining images and statistical methods to generate high-confidence single-cell spatial gene expression profiles for Stereo-seq data. STCellbin is an update of StereoCell, now using a more advanced cell segmentation technique, so more accurate cell boundaries can be obtained, allowing more reliable single-cell spatial gene expression profiles to be obtained. After peer review more comparisons were added and more description given on what was upgraded in this version to convince the reviewers. Demonstrating it is a more reliable method, particularly for analyzing high-resolution and large-field-of-view spatial transcriptomic data. And extending the capability to automatically process Stereo-seq cell membrane/wall staining images for identifying cell boundaries.

      This evaluation refers to version 2 of the preprint

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    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  3. BatchEval Pipeline: Batch Effect Evaluation Workflow for Multiple Datasets Joint Analysis

    This article has 6 authors:
    1. Chao Zhang
    2. Qiang Kang
    3. Mei Li
    4. Hongqing Xie
    5. Shuangsang Fang
    6. Xun Xu
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      For better data quality assessment of large spatial transcriptomics datasets this new BatchEval software has been developed as a batch effect evaluation tool. This generates a comprehensive report with assessment findings, including basic information of integrated datasets, a batch effect score, and recommended methods for removing batch effects. The report also includes evaluation details for the raw dataset and results from batch effect removal methods. Through peer review and clarification of a number of points it now looks convincing that this tool helps researchers identify and remove batch effects, ensuring reliable and meaningful insights from integrated datasets. Potentially making the tool valuable for researchers who need to analyze large datasets of this type, as it provides an easy and reliable way to assess data quality and ensures that downstream analyses are robust and reliable.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  4. Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

    This article has 20 authors:
    1. Magnus Wolf
    2. Bruno Lopes da Silva Ferrette
    3. Raphael T. F. Coimbra
    4. Menno de Jong
    5. Marcel Nebenfuehr
    6. David Prochotta
    7. Yannis Schöneberg
    8. Konstantin Zapf
    9. Jessica Rosenbaum
    10. Hannah A. Mc Intyre
    11. Julia Maier
    12. Clara C.S. de Souza
    13. Lucas M. Gehlhaar
    14. Melina J. Werner
    15. Henrik Oechler
    16. Marie Wittekind
    17. Moritz Sonnewald
    18. Maria A. Nilsson
    19. Axel Janke
    20. Sven Winter
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference analysis of the snake pipefish genome using this data enables tracing of population changes over the past 1 million years, and this reference will allow further analyses and studies relating these to changes in climate.

      **This evaluation refers to version 1 of the preprint

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    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  5. Species Composition and Distribution of Anopheles gambiae Complex Circulating in Kinshasa

    This article has 11 authors:
    1. Josue Zanga
    2. Emery Metelo
    3. Nono Mvuama
    4. Victoire Nsabatien
    5. Vanessa Mvudi
    6. Degani Banzulu
    7. Osée Mansiangi
    8. Maxwel Bamba
    9. Narcisse Basosila
    10. Rodrigue Agossa
    11. Roger Wumba
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment: Understanding the distribution of Anopheles mosquito species is essential for planning and implementing malaria control programmes, a task undertaken in this study that assesses the composition and distribution of the Anopheles in different districts of Kinshasa in the Democratic Republic of Congo. Mosquitoes were collected using CDC light traps, and then identified by morphological and molecular means. In total 3,839 Anopheles were collected, and data was digitised, validated and shared via the GBIF database under a CC0 waiver. The project monitoring the monthly dynamics of four species of Anopheles, showing a fluctuation in their respective frequencies during the study period. 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

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    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  6. Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities

    This article has 2 authors:
    1. Danielle C. Wrenn
    2. Devin M. Drown
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment: Antimicrobial resistance (AMR) is a global public health threat, and environmental microbial communities can act as reservoirs for resistance genes. There is a need for genomic surveillance could provide insights into how these reservoirs change and impact public health. With that goal in mind this study tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. On average adaptive sampling resulting in a target composition 4x higher than without adaptive sampling, and increased target yield in most replicates. The methods and scripts for this approach were reviewed and curated together, although the scope of this study was limited in terms of communities tested and AMR genes targeted. And the authors improved their analysis by conducting an additional analysis of a diverse microbial community. Demonstrating the method is reusable and its results are promising for developing a flexible, portable, and cost-effective AMR surveillance tool.

      *This evaluation refers to version 1 of the preprint

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    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  7. Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo

    This article has 18 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  8. A reference assembly for the legume cover crop, hairy vetch ( Vicia villosa )

    This article has 10 authors:
    1. Tyson Fuller
    2. Lisa M. Koch
    3. Lisa Kissing Kucek
    4. Shahjahan Ali
    5. Hayley Mangelson
    6. Timothy Hernandez
    7. Timothy P.L. Smith
    8. Derek M. Bickhart
    9. Heathcliffe Riday
    10. Michael L. Sullivan
    This article has been curated by 1 group:
    • 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

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    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  9. Genome assembly of the bearded iris Iris pallida Lam

    This article has 10 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  10. A Database of Restriction Maps to Expand the Utility of Bacterial Artificial Chromosomes

    This article has 6 authors:
    1. Eamon Winden
    2. Alejandro Vasquez-Echeverri
    3. Susana Calle-Casteneda
    4. Yumin Lian
    5. Juan Pablo Hernández-Ortiz
    6. David C. Schwartz
    This article has been curated by 1 group:
    • 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

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  11. Trumpet plots: Visualizing The Relationship Between Allele Frequency And Effect Size In Genetic Association Studies

    This article has 4 authors:
    1. Lucia Corte
    2. Lathan Liou
    3. Paul F. O’Reilly
    4. Judit García-González
    This article has been curated by 1 group:
    • 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. *

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  12. Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

    This article has 5 authors:
    1. Sagar Patel
    2. Zachary N. Harris
    3. Jason P. Londo
    4. Allison Miller
    5. Anne Fennell
    This article has been curated by 1 group:
    • 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.

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    This article has 2 evaluationsAppears in 4 listsLatest version Latest activity
  13. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

    This article has 9 authors:
    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
    This article has been curated by 1 group:
    • 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.

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  14. Mycobacterial Metabolic Model Development for Drug Target Identification

    This article has 3 authors:
    1. Bridget P. Bannerman
    2. Alex Oarga
    3. Jorge Júlvez
    This article has been curated by 1 group:
    • 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.

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    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity