Latest preprint reviews

1. 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

   Reviewed by GigaByte

2. 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. *

   Reviewed by GigaByte

3. 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.

   Reviewed by GigaByte

4. 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.

   Reviewed by GigaByte

5. 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.

   Reviewed by GigaByte

6. Genome assembly of the deep-sea coral Lophelia pertusa

   This article has 2 authors:

   1. Santiago Herrera
   2. Erik E. Cordes

   Reviewed by GigaByte

7. The first genome assembly of the amphibian nematode parasite ( Aplectana chamaeleonis )

   This article has 4 authors:

   1. Lei Han
   2. Tianlu Liu
   3. Fengping He
   4. Zhijun Hou

   Reviewed by GigaByte

8. PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects

   This article has 5 authors:

   1. Inês G. Gonçalves
   2. David A. Hormuth
   3. Sandhya Prabhakaran
   4. Caleb M. Phillips
   5. José Manuel García-Aznar

   Reviewed by GigaByte

9. Improvements to the Gulf Pipefish Syngnathus scovelli Genome

   This article has 10 authors:

   1. B Ramesh
   2. CM Small
   3. H Healey
   4. B Johnson
   5. E Barker
   6. M Currey
   7. S Bassham
   8. M Myers
   9. WA Cresko
   10. AG Jones

   Reviewed by GigaByte

10. Nanopore-based enrichment of antimicrobial resistance genes – a case-based study

    This article has 6 authors:

    1. Adrian Viehweger
    2. Mike Marquet
    3. Martin Hölzer
    4. Nadine Dietze
    5. Mathias W. Pletz
    6. Christian Brandt

    Reviewed by GigaByte