Evaluated articles

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

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

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

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

• 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

PhysiMeSS - a new physiCell addon for extracellular matrix modelling

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

• 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

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

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

• 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

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

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

• 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

Kinship analysis and pedigree reconstruction by RAD sequencing in cattle

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

• 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

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

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

• 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

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

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

• 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

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

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

• 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

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

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

• 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

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

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

• 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

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

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

• 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

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

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

• 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

Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

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 Diego 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. Tze Kiu Chong
17. Sean T.S. Law
18. Genome assembly and gene model prediction
19. Wenyan Nong
20. Genome analysis and quality control
21. Wenyan Nong
22. Sample collector and logistics
23. Tze Kiu Chong
24. Sean T.S. Law
25. Ho Yin Yip

• 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 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 presenting the first whole genome assembly of Dacryopinax spathularia, an edible mushroom-forming fungus that is used in the food industry to produce natural preservatives. Using PacBio and Omni-C data a 29.2 Mb genome was assembled, with a scaffold N50 of 1.925 Mb and 92.0% BUSCO score demonstrating the quality (review pushing the authors to provide more detail and QC stats to help better convince on this). This data providing a useful resource for further phylogenomic studies in the family Dacrymycetaceae and investigations on the biosynthesis of glycolipids with potential applications in the food industry.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Genome assembly of the milky mangrove Excoecaria agallocha

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 Diego 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. Sean T.S. Law
17. Wai Lok So
18. Genome assembly and gene model prediction
19. Wenyan Nong
20. Genome analysis and quality control
21. Wenyan Nong
22. Sample collector and logistics
23. David T.W. Lau
24. Sean T.S. Law
25. Shing Yip Lee
26. Ho Yin Yip

• 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 milky mangrove Excoecaria agallocha, also known as blind-your-eye mangrove due to its toxic properties of its milky latex that can cause blindness when it comes into contact with the eyes. Living in the brackish water of tropical mangrove forests from India to Australia, they are an extremely important habitat for a diverse variety of aquatic species, including the mangrove jewel bug of which this tree is the sole food source for the larvae. Using PacBio HiFi long-reads and Omni-C technology a 1,332.45 Mb genome was assembled, with 1,402 scaffolds and a scaffold N50 of 58.95 Mb. After feedback the annotations were improved, predicting a very high number (73,740) protein coding genes. The data presented here provides a valuable resource for further investigation in the biosynthesis of phytochemical compounds in its milky latex with the potential of many medicinal and pharmacological properties. As well as increasing the understanding of biology and evolution in genome architecture in the Euphorbiaceae family and mangrove species adapted to high levels of salinity.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific

1. Remy Gatins
2. Carlos F. Arias
3. Carlos Sánchez
4. Giacomo Bernardi
5. Luis F. De León

• Curated by GigaByte

  Editors Assessment:

  The King Angelfish (Holacanthus passer) is a great example of a Holacanthus angelfish that are some of the most iconic marine fishes of the Tropical Eastern Pacific. However, very limited genomic resources currently exist for the genus and these authors have assembled and annotated the nuclear genome of the species, and used it examine the demographic history of the fish. Using nanopore long reads to assemble a compact 583 Mb reference with a contig N50 of 5.7 Mb, and 97.5% BUSCOs score. Scruitinising the data, the BUSCO score was high compared to the initial N50’s, providing some useful lessons learned on how to get the most out of ONT data. The analysis suggests that the demographic history in H. passer was likely shaped by historical events associated with the closure of the Isthmus of Panama, rather than by the more recent last glacial maximum. This data provides a genomic resource to improve our understanding of the evolution of Holacanthus angelfishes, and facilitating research into local adaptation, speciation, and introgression of marine fishes. In addition, this genome can help improve the understanding of the evolutionary history and population dynamics of marine species in the Tropical Eastern Pacific.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart ( Sminthopsis crassicaudata )

1. Neke Ibeh
2. Charles Y. Feigin
3. Stephen R. Frankenberg
4. Davis J. McCarthy
5. Andrew J. Pask
6. Irene Gallego Romero

• Curated by GigaByte

  Editors Assessment: Marsupial species are invaluable for comparative studies due to their distinctive modes of reproduction and development, but there are a shortage of genomic resources to do these types of analyses. To help address that data gap multi-tissue transcriptomes and transcriptome assemblies have been sequenced and shared for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that due to is ease of breeding is emerging as a useful lab model. Using ONT nanopore and Pacbio long-reads and illumina short reads 2,093,982 transcripts were sequenced and assembled, and functional annotation of the assembled transcripts was also carried out. Some addition work was required to provide more details on the QC metrics and access to the data but this was resolved during review. This work ultimately producing dunnart genome assembly measuring 3.23 Gb in length and organized into 1,848 scaffolds, with a scaffold N50 value of 72.64 Mb. These openly available resources hopefully provide novel insights into the unique genomic architecture of this unusual species and provide valuable tools for future comparative mammalian studies.

  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

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