Evaluated articles

Molecular Property Diagnostic Suite for COVID-19 (MPDS ^COVID-19 ): An open access disease specific drug discovery portal

1. Lipsa Priyadarsinee
2. Esther Jamir
3. Selvaraman Nagamani
4. Hridoy Jyoti Mahanta
5. Nandan Kumar
6. Lijo John
7. Himakshi Sarma
8. Asheesh Kumar
9. Anamika Singh Gaur
10. Rosaleen Sahoo
11. S. Vaikundamani
12. N. Arul Murugan
13. U. Deva Priyakumar
14. G.P.S. Raghava
15. Prasad V. Bharatam
16. Ramakrishnan Parthasarathi
17. V. Subramanian
18. G. Madhavi Sastry
19. G. Narahari Sastry

• Curated by GigaByte

  Editors Assessment:

  MPDSCOVID-19 has been developed as a one-stop solution for drug discovery research for COVID-19, running on the Molecular Property Diagnostic Suite (MPDS) platform. This is built upon the open-source Galaxy workflow system, integrating many modules and data specific to COVID-19. Data integrated includes SARS-CoV-2 targets, genes and their pathway information; information on repurposed drugs against various targets of SARS-CoV-2, mutational variants, polypharmacology for COVID-19, drug-drug interaction information, Protein-Protein Interaction (PPI), host protein information, epidemiology, and inhibitors databases. After improvements to the technical description of the platform, testing helped demonstrate the potential to drive open-source computational drug discovery with the platform.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Molecular Property Diagnostic Suite for COVID-19 (MPDS ^COVID-19 ): An open access disease specific drug discovery portal

1. Lipsa Priyadarsinee
2. Esther Jamir
3. Selvaraman Nagamani
4. Hridoy Jyoti Mahanta
5. Nandan Kumar
6. Lijo John
7. Himakshi Sarma
8. Asheesh Kumar
9. Anamika Singh Gaur
10. Rosaleen Sahoo
11. S. Vaikundamani
12. N. Arul Murugan
13. U. Deva Priyakumar
14. G.P.S. Raghava
15. Prasad V. Bharatam
16. Ramakrishnan Parthasarathi
17. V. Subramanian
18. G. Madhavi Sastry
19. G. Narahari Sastry

• Curated by GigaByte

  Editors Assessment:

  MPDSCOVID-19 has been developed as a one-stop solution for drug discovery research for COVID-19, running on the Molecular Property Diagnostic Suite (MPDS) platform. This is built upon the open-source Galaxy workflow system, integrating many modules and data specific to COVID-19. Data integrated includes SARS-CoV-2 targets, genes and their pathway information; information on repurposed drugs against various targets of SARS-CoV-2, mutational variants, polypharmacology for COVID-19, drug-drug interaction information, Protein-Protein Interaction (PPI), host protein information, epidemiology, and inhibitors databases. After improvements to the technical description of the platform, testing helped demonstrate the potential to drive open-source computational drug discovery with the platform.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

An improved chromosome-level genome assembly of perennial ryegrass ( Lolium perenne L.)

1. Yutang Chen
2. Roland Kölliker
3. Martin Mascher
4. Dario Copetti
5. Axel Himmelbach
6. Nils Stein
7. Bruno Studer

• Curated by GigaByte

  Editors Assessment:

  This Data Release paper presents an updated genome assembly of the doubled haploid perennial ryegrass (Lolium perenne L.) genotype Kyuss (Kyuss v2.0). To correct for structural the authors de novo assembled the genome again with ONT long-reads and generated 50-fold coverage high-throughput chromosome conformation capture (Hi-C) data to assist pseudo-chromosome construction. After being asked for some more improvements to gene and repeat annotation the authors now demonstrate the new assembly is more contiguous, more complete, and more accurate than Kyuss v1.0 and shows the correct pseudo-chromosome structure. This more accurate data have great potential for downstream genomic applications, such as read mapping, variant calling, genome-wide association studies, comparative genomics, and evolutionary biology. These future analyses being able to benefit forage and turf grass research and breeding.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Citizen science data on urban forageable plants: a case study in Brazil

1. Filipi Miranda Soares
2. Luís Ferreira Pires
3. Maria Carolina Garcia
4. Lidio Coradin
5. Natalia Pirani Ghilardi-Lopes
6. Rubens Rangel Silva
7. Aline Martins de Carvalho
8. Anand Gavai
9. Yamine Bouzembrak
10. Benildes Coura Moreira dos Santos Maculan
11. Sheina Koffler
12. Uiara Bandineli Montedo
13. Debora Pignatari Drucker
14. Raquel Santiago
15. Maria Clara Peres de Carvalho
16. Ana Carolina da Silva Lima
17. Hillary Dandara Elias Gabriel
18. Stephanie Gabriele Mendonça de França
19. Karoline Reis de Almeida
20. Bárbara Junqueira dos Santos
21. Antonio Mauro Saraiva

• Curated by GigaByte

  Editors Assessment:

  This is a Data Release paper describing data sets derived from the Pomar Urbano project cataloging edible fruit-bearing plants in Brazil. Including data sourced from the citizen science iNaturalist app, tracking the distribution and monitoring of these plants within urban landscapes (Brazilian state capitals). The data was audited and peer reviewed and put into better context, and there is a companion commentary in GigaScience journal better explaining the rationale for the study. Demonstrating this data providing a platform for understanding the diversity of fruit-bearing plants in select Brazilian cities and contributing to many open research questions in the existing literature on urban foraging and ecosystem services in urban environments.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

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

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

• 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

Reviewed by GigaByte

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

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

• 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

Reviewed by GigaByte

BatchEval Pipeline: Batch Effect Evaluation Workflow for Multiple Datasets Joint Analysis

1. Chao Zhang
2. Qiang Kang
3. Mei Li
4. Hongqing Xie
5. Shuangsang Fang
6. Xun Xu

• 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

Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

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

• 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

Reviewed by GigaByte

Species Composition and Distribution of Anopheles gambiae Complex Circulating in Kinshasa

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

• 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

Reviewed by GigaByte

Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities

1. Danielle C. Wrenn
2. Devin M. Drown

• 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

Reviewed by GigaByte

Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo

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

• 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

A reference assembly for the legume cover crop, hairy vetch ( Vicia villosa )

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

• 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

Reviewed by GigaByte

Genome assembly of the bearded iris Iris pallida Lam

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

• 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

A Database of Restriction Maps to Expand the Utility of Bacterial Artificial Chromosomes

1. Eamon Winden
2. Alejandro Vasquez-Echeverri
3. Susana Calle-Casteneda
4. Yumin Lian
5. Juan Pablo Hernández-Ortiz
6. David C. Schwartz

• 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

Trumpet plots: Visualizing The Relationship Between Allele Frequency And Effect Size In Genetic Association Studies

1. Lucia Corte
2. Lathan Liou
3. Paul F. O’Reilly
4. Judit García-González

• 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

Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

1. Sagar Patel
2. Zachary N. Harris
3. Jason P. Londo
4. Allison Miller
5. Anne Fennell

• 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

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

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

• 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

Mycobacterial Metabolic Model Development for Drug Target Identification

1. Bridget P. Bannerman
2. Alex Oarga
3. Jorge Júlvez

• 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

Genome assembly of the deep-sea coral Lophelia pertusa

1. Santiago Herrera
2. Erik E. Cordes

Reviewed by GigaByte

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

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

Reviewed by GigaByte