GigaByte

Latest preprint reviews

1. Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny

   This article has 3 authors:

   1. Marcel Nebenführ
   2. Ulfur Arnason
   3. Axel Janke

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     Due to them being found in the landlocked, isolated habitat of Lake Baikal makes the Baikal Seal (Pusa sibirica) unique among all pinnipeds as the only freshwater seal. This paper presents reference-based assemblies of six newly sequenced Baikal seal individuals, one individual of the ringed seal, as well as the first short-read data of the harbor seal and the Caspian seal . This data aiding the study of the genomic diversity of the Baikal seal and to contribute baseline data to the limited genomic data available for seals. Peer review extended the description of the used tools and parameters in the revised manuscript, and provided some more information on the methods..This newly generated sequencing data hopefully now helps to extend the phylogeny of the Phoca/Pusa group on genome-wide data and can also broaden the view into the genetic structure and diversity of the Baikal seal

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

2. TSTA: thread and SIMD-based trapezoidal pairwise/multiple sequence-alignment method

   This article has 4 authors:

   1. Peiyu Zong
   2. Wenpeng Deng
   3. Jian Liu
   4. Jue Ruan

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     The article presents strategies for accelerating sequence alignment using multithreading and SIMD (Single Instruction, Multiple Data) techniques, and introduces a new algorithm called TSTA (Thread and SIMD-Based Trapezoidal Pairwise/Multiple Sequence-Alignment). The Technical Release write-up presenting a detailed description of TSTA's performance in pairwise sequence alignment (PSA) and multiple sequence alignment (MSA), and compares it with various existing alignment algorithms. Demonstrating the performance gains achieved by vectorized SIMD technology and the application of threading. Testing and debugging a few errors, and adding some more background detail, demonstrating it can achieve faster comparison speed. Demonstrating TSTA's efficacy in pairwise sequence alignment and multiple sequence alignment, particularly with long reads, and showcasing considerable speed enhancements compared to existing tools.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

3. Chromosome-level genome assembly and annotation of the crested gecko, Correlophus ciliatus, a lizard incapable of tail regeneration

   This article has 3 authors:

   1. Marc A. Gumangan
   2. Zheyu Pan
   3. Thomas P. Lozito

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     The crested gecko (Correlophus ciliatus), is a lizard species endemic to New Caledonia, and a potentially interesting model organism due to its unusual (for a gecko) inability to regenerate amputated tails. With that in mind here is presented a new reference genome for the species, assembled using PacBio Sequel II platform and Dovetail Omni-C libraries. Producing a genome with a total size of 1.65 Gb, 152 scaffolds, a L50 of 6, and N50 of 109 Mb. Peer review making sure more detail was added on data acquisition and processing to enhance reproducibility. In the end producing potentially useful data for studying the genetic mechanisms involved in loss of tail regeneration.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

4. SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds

   This article has 18 authors:

   1. Paolo Cozzi
   2. Arianna Manunza
   3. Johanna Ramirez-Diaz
   4. Valentina Tsartsianidou
   5. Konstantinos Gkagkavouzis
   6. Pablo Peraza
   7. Anna Maria Johansson
   8. Juan José Arranz
   9. Fernando Freire
   10. Szilvia Kusza
   11. Filippo Biscarini
   12. Lucy Peters
   13. Gwenola Tosser-Klopp
   14. Gabriel Ciappesoni
   15. Alexandros Triantafyllidis
   16. Rachel Rupp
   17. Bertrand Servin
   18. Alessandra Stella

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This paper presents the SMARTER database, a collection of tools and scripts to gather, standardize, and share with the scientific community a comprehensive dataset of genomic data and metadata information on worldwide small ruminant populations. Which has come out of the EU multi-actor (12 country) H2020 project called SMARTER: SMAll RuminanTs breeding for Efficiency and Resilience. This bringing together genotypes for about 12,000 sheep and 6,000 goats, alongside phenotypic and geographic information. The paper providing insight into how the database was put together, presenting the code for the SMARTER—frontend, backend and API, alongside instructions for users. Peer review tested the platform and provided suggestions on improving the metadata. Demonstrating the project provides valuable information on sheep and goat populations around the world, that can be an essential tool for ruminant researchers. Enabling them to generate new insights and offer the possibility to store new genotypes and drive progress in the field.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

5. NucBalancer: streamlining barcode sequence selection for optimal sample pooling for sequencing

   This article has 2 authors:

   1. Saurabh Gupta
   2. Ankur Sharma

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This paper presents NucBalancer, a R-pipeline and Shiny app designed for the optimal selection of barcode sequences for sample multiplexing in sequencing. Providing a user-friendly interface aiming to make this process accessible to both bioinformaticians and experimental researchers, enhancing its utility in adapting libraries prepared for one sequencing platform to be compatible with others. Important now with the introduction of additional sequencing platforms by Element Biosciences (AVITI System) and Ultima Genomics (UG100) increasing the diversity and capability of genomic research tools available. NucBalancer’s incorporation of dynamic parameters, including customizable red flag thresholds, allows for precise and practical barcode sequencing strategies. This adaptability is key in ensuring uniform nucleotide distribution, particularly in MGI sequencing and single-cell genomic studies, leading to more reliable and cost-effective sequencing outcomes across various experimental conditions. All the code is available under an open source license, and upon review the authors have also shared the code for the Shiny app.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

6. V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation

   This article has 19 authors:

   1. Lara Fuhrmann
   2. Kim Philipp Jablonski
   3. Ivan Topolsky
   4. Aashil A Batavia
   5. Nico Borgsmüller
   6. Pelin Icer Baykal
   7. Matteo Carrara
   8. Chaoran Chen
   9. Arthur Dondi
   10. Monica Dragan
   11. David Dreifuss
   12. Anika John
   13. Benjamin Langer
   14. Michal Okoniewski
   15. Louis du Plessis
   16. Uwe Schmitt
   17. Franziska Singer
   18. Tanja Stadler
   19. Niko Beerenwinkel

   Reviewed by GigaScience, GigaByte

7. 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

8. 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

9. 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

10. 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