Latest preprint reviews

1. Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research

   This article has 4 authors:

   1. Locedie Mansueto
   2. Tobias Kretzschmar
   3. Ramil Mauleon
   4. Graham J. King

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This paper reports the establishment of the International Cannabis Genomics Research Consortium (ICGRC) web portal leveraging the open source Tripal platform to enhance data accessibility and integration for Cannabis sativa (Cannabis) multi-omics research. With the aim of bringing together the wealth of publicly available genomic, transcriptomic, proteomic, and metabolomic data sets to improve cannabis for food, fiber and medicinal traits. Tripal is a content management system for genomics data, presenting a ready-to-use specialized ‘omics modules for loading, visualization, and analysis, and is GMOD (Generic Model Organism Database) standards-compliant. The paper explaining how this was put together, what data and features are available, and providing a case study for other communities wanting to create their own Tripal platform. Covering their setup and customizations of the Tripal platform, and how they re-engineered modules for multi-omics data integration, and addition of many other custom features that can be reused. Peer review fixed a few minor bugs and added clarifications on how the platform will be updated.

     *This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

2. PhysiMeSS - a new physiCell addon for extracellular matrix modelling

   This article has 4 authors:

   1. Vincent Noël
   2. Marco Ruscone
   3. Robyn Shuttleworth
   4. Cicely K. Macnamara

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     PhysiCell is an open source multicellular systems simulator for studying many interacting cells in dynamic tissue microenvironments. As part of the PhysiCell ecosystem of tools and modules this paper presents a PhysiCell addon, PhysiMeSS (MicroEnvironment Structures Simulation) which allows the user to accurately represent the extracellular matrix (ECM) as a network of fibres. This can specify rod-shaped microenvironment elements such as the matrix fibres (e.g. collagen) of the ECM, allowing the PhysiCell user the ability to investigate physical interactions with cells and other fibres. Reviewers asked for additional clarification on a number of features. And the paper now clear future releases will provide full 3D compatibility and include working on fibrogenesis, i.e. the creation of new ECM fibres by cells.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

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

   This article has 7 authors:

   1. Renato Santos
   2. Victor 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

10. 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