Latest preprint reviews

1. High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog’s genome

   This article has 8 authors:

   1. Marcel Nebenführ
   2. David Prochotta
   3. Alexander Ben Hamadou
   4. Axel Janke
   5. Charlotte Gerheim
   6. Christian Betz
   7. Carola Greve
   8. Hanno Jörn Bolz

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This Data Release paper presents the genome of the whippet breed of dog. Demonstrating a streamlined laboratory and bioinformatics workflows with PacBio HiFi long-read whole-genome sequencing that enables the generation of a high-quality reference genome within one week. The genome study being a collaboration between an academic biodiversity institute and a medical diagnostic company. The presented method of working and workflow providing examples that can be used for a wide range of future human and non-human genome projects. The final is 2.47 Gbp assembly being of high quality - with a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. This reference being scaffolded into 39 chromosome-length scaffolds and the annotation resulting in 28,383 transcripts. The results also looked at the Myostatin gene which can be used for breeding purposes, as these heterozygous animals can have an advantage in dog races. The reviewers making the authors clarify this part a little better with additional results. Overall this study demonstrating how rapidly animal genome research can be carried out through close and streamlined time management and collaboration.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

2. RiboSnake – a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis

   This article has 9 authors:

   1. Ann-Kathrin Dörr
   2. Josefa Welling
   3. Adrian Dörr
   4. Jule Gosch
   5. Hannah Möhlen
   6. Ricarda Schmithausen
   7. Jan Kehrmann
   8. Folker Meyer
   9. Ivana Kraiselburd

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This new software paper presents RiboSnake, a validated, automated, reproducible analysis pipeline implemented in the popular Snakemake workflow management system for microbiome analysis. Analysing16S rRNA gene amplicon sequencing data, this uses the widely used oQIIME2 [ tool as the basis of the workflow as it offers a wide range of functionality. Users of QIIME2 can be overwhelmed by the number of options at their disposal, and this workflow provides a fully automated and fully reproducible pipeline that can be easily installed and maintained. Providing an easy-to-navigate output accessible to non bioinformatics experts, alongside sets of already validated parameters for different types of samples. Reviewers requested some clarification for testing, worked examples and documentation, and this was improved to produce a convincingly easy-to-use workflow. Hopefully opening up an already very established technique to a new group of users and assisting them with reproducible science.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

3. Kinship analysis and pedigree reconstruction by RAD sequencing in cattle

   This article has 8 authors:

   1. Yiming Xu
   2. Wanqiu Wang
   3. Jiefeng Huang
   4. Minjie Xu
   5. Binhu Wang
   6. Yingsong Wu
   7. Yongzhong Xie
   8. Jianbo Jian

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     RAD-Seq (Restriction-site-associated DNA sequencing) is a cost-effective method for single nucleotide polymorphism (SNP) discovery and genotyping. In this study the authors performed a kinship analysis and pedigree reconstruction for two different cattle breeds (Angus and Xiangxi yellow cattle). A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping using RAD-Seq. Producing a SNP panel with 7305 SNPs capturing the maximum difference between paternal and maternal genome information, and being able to distinguish between the F1 and F2 generation with 90% accuracy. Peer review helped highlight better the practical applications of this work. The combination of the efficiency of RNA-seq and advances in kinship analysis here can helpfully help improve breed management, local resource utilization, and conservation of livestock.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

4. Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor

   This article has 20 authors:

   1. Hong Kong Biodiversity Genomics Consortium
   2. Jerome H.L. Hui
   3. Ting Fung Chan
   4. Leo L. Chan
   5. Siu Gin Cheung
   6. Chi Chiu Cheang
   7. James K.H. Fang
   8. Juan Diego Gaitan-Espitia
   9. Stanley C.K. Lau
   10. Yik Hei Sung
   11. Chris K.C. Wong
   12. Kevin Y.L. Yip
   13. Yingying Wei
   14. Wai Lok So
   15. Wenyan Nong
   16. Sean T.S. Law
   17. Paul Crow
   18. Aiko Leong
   19. Liz Rose-Jeffreys
   20. Ho Yin Yip

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment: This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong (see https://doi.org/10.46471/GIGABYTE_SERIES_0006). This example assembles the genome of the black-faced spoonbill (Platalea minor), an emblematic wading bird from East Asia that is classified as globally endangered by the IUCN. This Data Release reporting a 1.24Gb chromosomal-level genome assembly produced using a combination of PacBio SMRT and Omni-C scaffolding technologies. BUSCO and Merqury validation were carried out, gene models created, and peer reviewers also requested MCscan synteny analysis. This showed the genome assembly had high sequence continuity with scaffold length N50=53 Mb. Presenting data from 14 individuals this will hopefully be a useful and valuable resources for future population genomic studies aimed at better understanding spoonbill species numbers and conservation.

     *This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

5. Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis

   This article has 7 authors:

   1. Caroline A. McCormick
   2. Stuart Akeson
   3. Sepideh Tavakoli
   4. Dylan Bloch
   5. Isabel N. Klink
   6. Miten Jain
   7. Sara H. Rouhanifard

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     Oxford nanopore direct RNA sequencing (DRS) is a relatively new sequencing technology enabling measurements of RNA modifications. In vitro transcription (IVT)-based negative controls (i.e. modification-free transcripts) are a practical and targeted control for this direct sequencing, providing a baseline measurement for canonical nucleotides within a matched and biologically-derived sequence context. This work presents exactly this type of a long-read, multicellular, poly-A RNA-based, IVT-derived, unmodified transcriptome dataset. Review flagging more statistical analyses needed be performed for the data quality, and this was provided. The resulting data providing a resource to the direct RNA analysis community, helping reduce the need for expensive IVT library preparation and sequencing for human samples. And also serving as a framework for RNA modification analysis in other organisms.

     This evaluation refers to version 1 and 2 of the preprint

   Reviewed by GigaByte

6. PhysiCell Studio: a graphical tool to make agent-based modeling more accessible

   This article has 8 authors:

   1. Randy Heiland
   2. Daniel Bergman
   3. Blair Lyons
   4. Julie Cass
   5. Heber L. Rocha
   6. Marco Ruscone
   7. Vincent Noël
   8. Paul Macklin

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This paper presents a new tool to make using PhysiCell easier, which is an open-source, physics-based multicellular simulation framework with a very wide user base. PhysiCell Studio is a graphical tool that makes it easier to build, run, and visualize PhysiCell models. Over time, it has evolved from being a GUI to include many additional functionalities, and can be used as desktop and cloud versions. This paper outlines the many features and functions, the design and development process behind it, and deployment instructions. Peer review improved the organisation of the various repositories and adding both a requirements.txt and environment.yml files. Looking to the future the developers are planning to add new features based on community feedback and contributions, and this paper presents the many code repositories if readers wish to contribute to the development process.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

7. Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients

   This article has 7 authors:

   1. Renato Santos
   2. Víctor Moreno-Torres
   3. Ilduara Pintos
   4. Octavio Corral
   5. Carmen de Mendoza
   6. Vicente Soriano
   7. Manuel Corpas

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     Many studies have explored the genetic determinants of COVID-19 severity, these GWAS studies using microarrays or expensive whole-genome sequencing (WGS). Low-coverage WGS data can be imputed using reference panels to enhance resolution and statistical power while maintaining much lower costs, but imputation accuracy is difficult to balance. This work demonstrates how to address these challenges utilising the GLIMPSE1 algorithm, a less resource-intensive tool that produces more accurate imputed data than its predecessors. Generating a dataset containing 79 imputed low-coverage WGS samples from patients with severe COVID-19 symptoms during the initial wave of the SARS-CoV-2 pandemic in Spain. The validation of this imputation and filtering process shows that GLIMPSE1 can be confidently used to impute variants with minor allele frequency up to approximately 2%. After peer review the authors clarified and provided more validation and statistics and figures to help convince this approach was valid. This work showcasing the viability of using low-coverage WGS imputation to generate data for the study of disease-related genetic markers, alongside a validation methodology to ensure the accuracy of the data produced. Helping inspire confidence and encouraging others to deploy similar approaches to other infectious diseases, genetic disorders, or population-based genetic studies. Particularly in large-scale genomic projects and resource-limited settings where sequencing at higher coverage could prove to be prohibitively expensive.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

8. Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

   This article has 21 authors:

   1. Hong Kong Biodiversity Genomics Consortium
   2. Jerome H.L. Hui
   3. Ting Fung Chan
   4. Leo L. Chan
   5. Siu Gin Cheung
   6. Chi Chiu Cheang
   7. James K.H. Fang
   8. Juan D. Gaitan-Espitia
   9. Stanley C.K. Lau
   10. Yik Hei Sung
   11. Chris K.C. Wong
   12. Kevin Y.L. Yip
   13. Yingying Wei
   14. Wai Lok So
   15. Wenyan Nong
   16. Hydrogen S.F. Pun
   17. Wing Kwong Yau
   18. Colleen Y.L. Chiu
   19. Sammi S.S. Chan
   20. Kacy K.L. Man
   21. Ho Yin Yip

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presents the genome of the golden birdwing butterfly Troides aeacus (Lepidoptera, Papilionidae). A notable and popular species in Asia that faces habitat loss due to urbanization and human activities. The lack of genomic resources impedes conservation efforts based on genetic markers, as well as better understanding of its biology. Using PacBio HiFi long reads and Omni-C a 351Mb genome was assembled genome anchored to 30 pseudo-molecules. After reviewers requested more information on the genome quality it seems there was high sequence continuity with contig length N50 = 11.67 Mb and L50 = 14, and scaffold length N50 = 12.2 Mb and L50 = 13. Allowing a total of 24,946 protein-coding genes were predicted. This study presents the first chromosomal-level genome assembly of the golden birdwing T. aeacus, a potentially useful resource for further phylogenomic studies of birdwing butterfly species in terms of species diversification and conservation. This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

9. Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

   This article has 25 authors:

   1. Hong Kong Biodiversity Genomics Consortium
   2. Project Coordinator and Co-Principal Investigators
   3. Jerome H.L. Hui
   4. Ting Fung Chan
   5. Leo L. Chan
   6. Siu Gin Cheung
   7. Chi Chiu Cheang
   8. James K.H. Fang
   9. Juan D. Gaitan-Espitia
   10. Stanley C.K. Lau
   11. Yik Hei Sung
   12. Chris K.C. Wong
   13. Kevin Y.L. Yip
   14. Yingying Wei
   15. DNA extraction, library preparation and sequencing
   16. Franco M.F. Au
   17. Wai Lok So
   18. Genome assembly and gene model prediction
   19. Wenyan Nong
   20. Gene family annotation
   21. Ming Fung Franco Au
   22. Samples collectors
   23. Tin Yan Hui
   24. Brian K.H. Leung
   25. Gray A. Williams

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the common chiton, Liolophura japonica (Lischke, 1873). Chitons are marine molluscs that can be found worldwide from cold waters to the tropics that play important ecological roles in the environment, but to date are lacking in genomes with only a few assemblies available. This data was produced using PacBio HiFi reads and Omni-C sequencing data, the resulting genome assembly being around 609 Mb in size. From this 28,010 protein-coding genes were predicted. After review improved the methodological details the quality metrics look near chromosome-level, having a scaffold N50 length of 37.34 Mb and 96.1% BUSCO score. This high-quality genome should hopefully be a valuable resource for gaining new insights into the environmental adaptations of L. japonica in residing the intertidal zones and for future investigations in the evolutionary biology in Polyplacophorans and other molluscs.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

10. Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

    This article has 22 authors:

    1. Hong Kong Biodiversity Genomics Consortium
    2. Project Coordinator and Co-Principal Investigators
    3. Jerome H.L. Hui
    4. Ting Fung Chan
    5. Leo L. Chan
    6. Siu Gin Cheung
    7. Chi Chiu Cheang
    8. James K.H. Fang
    9. Juan D. Gaitan-Espitia
    10. Stanley C.K. Lau
    11. Yik Hei Sung
    12. Chris K.C. Wong
    13. Kevin Y.L. Yip
    14. Yingying Wei
    15. DNA extraction, library preparation and sequencing
    16. Wai Lok So
    17. Genome assembly and gene model prediction
    18. Wenyan Nong
    19. Sample collector, animal culture and logistics
    20. Apple P.Y. Chui
    21. Thomas H.W. Fong
    22. Ho Yin Yip

    This article has been curated by 1 group:

    • Curated by GigaByte

      Editors Assessment:

      This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the long-spined sea urchin Diadema setosum (Leske, 1778). Using PacBio HiFi long-reads and Omni-C data the assembled genome size was 886 Mb, consistent to the size of other sea urchin genomes. The assembly anchored to 22 pseudo-molecules/chromosomes, and a total of 27,478 genes including 23,030 protein-coding genes were annotated. Peer review added more to the conclusion and future perspectives. The data hopefully providing a valuable resource and foundation for a better understanding of the ecology and evolution of sea urchins.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte