Evaluated articles

Chromosome-level genome assemblies of five Sinocyclocheilus species

1. Chao Bian
2. Ruihan Li
3. Yuqian Ouyang
4. Junxing Yang
5. Xidong Mu
6. Qiong Shi

• Curated by GigaByte

  **Editors Assessment: ** Sinocyclocheilus are a genus of freshwater cavefish fish that are endemic to the Karst regions of Southwest China. Having diverse traits in morphology, behavior, and physiology typical of cavefish, that make them interesting models for studying cave adaptation and phylogenetic evolution. The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. Assembling S. grahami (the golden-line barbel), using PacBio and Hi-C sequencing technologies, a final chromosome-level genome assembly was 1.6 Gb in size with a contig N50 of 738.5 kb and a scaffold N50 of 30.7 Mb. With 93.1% of the assembled genome sequences and 93.8% of the predicted genes anchored onto 48 chromosomes. Subsequently the authors conducted a homologous comparison to obtain chromosome-level genome assemblies for four other Sinocyclocheilus species: S. maitianheensis, S. rhinocerous, S. anshuiensis, and S. Anophthalmus. With over 82% of the genome sequences anchored on these constructed chromosomes. Peer review provided clarification on the assembly strategy and provided more benchmarking. This data having the potential to contribute to species conservation and the exploitation of potential economic and ecological values of diverse Sinocyclocheilus members.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

1. Hewei Liang
2. Yuanqiang Zou
3. Mengmeng Wang
4. Tongyuan Hu
5. Haoyu Wang
6. Wenxin He
7. Yanmei Ju
8. Ruijin Guo
9. Junyi Chen
10. Fei Guo
11. Tao Zeng
12. Yuliang Dong
13. Yuning Zhang
14. Bo Wang
15. Chuanyu Liu
16. Xin Jin
17. Wenwei Zhang
18. Xun Xu
19. Liang Xiao

• Curated by GigaByte

  Editors Assessment:

  With the recent official launch of BGI’s new CycloneSEQ sequencing platform that delivers long-reads using novel nanpores, this paper presents benchmarking data and validation studies comparing short, long-rea data from other platforms and hybrid assemblies. This study tests the performance of the new platform in sequencing diverse microbial genomes, presenting raw and processed data to enable others to scrutinise and verify the work. Being openly peer-reviewed, and having scripts and protocols also shared for the first time helps provide transparency in this benchmarking process to increase trust in this new technology. On top of benchmarking typed strains, the technology also was tested with complex microbial communities. Yielding complete metagenome-assembled genomes (MAGs) which were not achieved by short- or long-read assemblies alone. By directly reading DNA molecules without fragmentation, the study demonstrating CycloneSEQ delivers long-read data with impressive length and accuracy, unlocking gaps that short-read technologies alone cannot bridge. Future work is expanding to real samples, with and fine-tuning the balance between short-read and long-read data for even faster, higher-quality assemblies.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

A single-molecule nanopore sequencing platform

1. Jia-Yuan Zhang
2. Yuning Zhang
3. Lele Wang
4. Fei Guo
5. Quanxin Yun
6. Tao Zeng
7. Xu Yan
8. Lei Yu
9. Lei Cheng
10. Wei Wu
11. Xiao Shi
12. Junyi Chen
13. Yuhui Sun
14. Jingnan Yang
15. Rongrong Guo
16. Xianda Zhang
17. Liu’er Kong
18. Zong’an Wang
19. Junlei Yao
20. Yangsheng Tan
21. Liuxin Shi
22. Zhentao Zhao
23. Zhongwang Feng
24. Xiaopeng Yu
25. Chuang Li
26. Wu Zhan
27. Yulin Ren
28. Fan Yang
29. Zhenjun Liu
30. Guangnan Fan
31. Weilian Zhong
32. Dachang Li
33. Lei He
34. Yanwei Qi
35. Meng Zhang
36. Yening Zhu
37. Heng Chi
38. Ziyu Zhao
39. Zhuofang Wei
40. Ziqi Song
41. Yanmei Ju
42. Ruijin Guo
43. Liang Xiao
44. Xiumei Lin
45. Liang Chen
46. Chentao Yang
47. Qiye Li
48. Ou Wang
49. Xin Jin
50. Ming Ni
51. Wenwei Zhang
52. Longqi Liu
53. Ying Gu
54. Jian Wang
55. Yuxiang Li
56. Xun Xu
57. Yuliang Dong

Reviewed by GigaByte

Genome assembly and annotation of Acropora pulchra from Mo’orea French Polynesia

1. Trinity Conn
2. Jill Ashey
3. Ross Cunning
4. Hollie M. Putnam

• Curated by GigaByte

  Editors Assessment:

  Acropora pulchra is a species small polyped stony corals in the family Acroporidae from the the Indo-Pacific. This Data Release is the first study in stony corals to present the DNA methylome in tandem with a high-quality genome assembled utilizing PacBio long-read HiFi sequencing. Sequencing an A. pulchra specimen from Mo’orea, French Polynesia. From this single molecule sequencing data DNA methylation data was also called and quantified, and additional short-read Illumina RNASeq data was used for gene annotation. This producing an assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp, and 40,518 protein-coding genes called. Peer review requested some improved benchmarking, and it is impressive to see from the results that the genome assembly represents the most complete and contiguous stony coral genome assembly to date. As an important indicator species and this data will hopefully serve as a resource to the coral and wider scientific community. Further quantification of the genome-wide methylation is needed aid the study epigenetics of non-model organisms, and specifically future analyses on methylation in coral.

  *This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics

1. Niema Moshiri

• Curated by GigaByte

  Editors Assessment:

  As volumes of viral and bacterial sequence data grow exponentially, the field of computational phylogenetics now demands resources to manage the burgeoning scale of this input data. This study introduces CompactTree, a C++ library designed for ultra-large phylogenetic trees with millions of tips. To address these scalability issues while maintaining ease of incorporation into external code bases, CompactTree is a header-only library with enhanced performance utilizing minimal dependencies, optimized node representation, and memory-efficient tree structure schemes. Resulting in significantly reduced memory footprints and improved processing times. Peer review requested some more detail on the functionality and some real-world examples, demonstrating the current utility of the tool. Although primarily supporting the (text-based) Newick format, the increased and extensibility scalability holds promise for multiple biological and epidemiological applications supporting more complex formats such as Nexus and NeXML. The tool is open source (GPLv3 licensed) and available in GitHub: https://niema.net/CompactTree

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species

1. Ma. Carmel F. Javier
2. Albert C. Noblezada
3. Persie Mark Q. Sienes
4. Robert S. Guino-o
5. Nadia Palomar-Abesamis
6. Maria Celia D. Malay
7. Carmelo S. del Castillo
8. Victor Marco Emmanuel N. Ferriols

• Curated by GigaByte

  Editors Assessment:

  The Visayan spotted deer (Rusa alfredi), is a small, endangered, primarily nocturnal species of deer found in the rainforests of the Visayan Islands in the Philippines. The present study reports the first draft genome assembly for the species, addressing a critical gap in genomic data for this IUCN-redlisted cervid. Using Illumina sequencing, the resulting genome assembly spans 2.52 Gb in size with a BUSCO completeness score of 95.5% and encompasses 24,531 annotated genes. Phylogenetic analysis suggests a close evolutionary relationship between R. alfredi and Cervus species suggesting that the genus Rusa is sister to Cervus. Peer-review teased out more benchmarking results and the annotation files, demonstrating this genomic resource is useful and usable for advancing population genetics and evolutionary studies, thereby informing conservation strategies and enhancing breeding programs for the critically threatened species. Providing whole genome sequences for other native species of Rusa could further provide genomic resources for detecting hybrids, which will also help the management and monitoring of these species, especially for the reintroduction of captive populations in the wild.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

1. Eleanore J. Ritter
2. Noé Cochetel
3. Andrea Minio
4. Peter Cousins
5. Dario Cantu
6. Chad Niederhuth

• Curated by GigaByte

  Editors Assessment:

  Teinturier grapes produce berries with pigmented skin and flesh, and are used in red wine blends, as they provide a deeper colour. This paper presents the genomes of two popular teinturier varieties (Dakapo and Rubired); sequenced, assembled, and annotated to provide additional resources for their use in breeding. Combining Nanopore and Illumina sequencing for Dakapo, scaffolding to the existing grapevine assembly to generate a final assembly of 508.5 Mbp and 36,940 gene annotations. For Rubired PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long and 56,681 genes annotated. Peer review has helped validate their high quality, these genomes hopefully enabling more insight into the genetics of grapevine berry colour and their other traits like frost and mildew-resistance.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

SqueezeCall: nanopore basecalling using a Squeezeformer network

1. Zhongxu Zhu

• Curated by GigaByte

  Editors Assessment:

  The accuracy of basecalling of nanopore sequencing still needs to be improved. With recent advances in deep learning this paper introduces SqueezeCall, a novel end-to-end tool for accurate basecalling. This uses Squeezeformer-achitecture which integrates local context extraction through convolutional layers and long-range dependency modeling via global context acquisition. Testing and peer review demonstrated that SqueezeCall outperformed traditional RNN and Transformer-based basecallers across multiple datasets, indicating its potential to refine genomic assembly and facilitate direct detection of modified bases in future genomic analytics. Future work is ongoing that will focus on training on highly curated datasets, including known modifications, to further increase research value. SqueezeCall is MIT licensed and available from GitHub here: https://github.com/labcbb/SqueezeCall

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine

1. Deruilin Liu
2. Demin Xu
3. Liuxin Shi
4. Jiayuan Zhang
5. Kewei Bi
6. Bei Luo
7. Chen Liu
8. Yuxiang Li
9. Guangyi Fan
10. Wen Wang
11. Zhi Ping

• Curated by GigaByte

  Editors Assessment:

  DNA has huge potential as a data storage medium because of its incredibly high storage density and stability. This work addresses the potential of modified bases, specifically 5-methylcytosine (5mC), in enhancing DNA data storage systems. This paper introduces a transcoding scheme named R+, which incorporates this modified 5mC base to increase information density beyond the standard limits. By encoding various file types into DNA sequences of between 1.3 to 1.6 kb in size, this method achieves an average recovery rate of 98.97% (with reference), validating the effectiveness of the method. On top of a wet-lab protocol (hosted in protocols.io) for the experimental validation of the transcoding scheme, it also includes open source code for in-silico simulation tests. Peer review scruitinising the protocols and validation are reusable and provide convincing results. As nanopore sequencing has enabled reading of these modified bases, it is timely making them applicable as extra letters in the molecular alphabet for DNA data storage

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Polyploid genome assembly of Cardamine chenopodiifolia

1. Aurélia Emonet
2. Mohamed Awad
3. Nikita Tikhomirov
4. Maria Vasilarou
5. Miguel Pérez-Antón
6. Xiangchao Gan
7. Polina Yu. Novikova
8. Angela Hay

• Curated by GigaByte

  This evaluation refers to version 1 of the preprint

  This work presents the genome of Cardamine chenopodiifolia, an amphicarpic plant (developing two fruit types, one above and another below ground) in the mustard (Brassicaceae) family. Cardamines also known as bittercresses and toothworts. As an octoploid species it has been challenging to create a genome reference for this species, and in this case the authors finally managed to achieve this using PacBio HiFi long-reads and Omni-C technology to assemble a fully phased, chromosome-level genome. Obtaining a 597Mb genome assembled into 32 phased chromosomes (plus mitochondrial and plastid genomes), and only having one gap in the centromeric region of chromosome 9. Peer review asked for additional QC and benchmarking, helping demonstrate the genome quality was very high, with only one gap and a N50 of 18.80Mb. The data presented here potentially helping to develop this species as an emerging model organism in the Brassicaceae for studying the development and evolution of amphicarpy by allopolyploidy.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids

1. Emma Gairin
2. Saori Miura
3. Hiroki Takamiyagi
4. Marcela Herrera
5. Vincent Laudet

• Curated by GigaByte

  Editors Assessment:

  Among hot topics in coral reef research, the difference between anemonefish and other damselfish is currently a popular area of research. In this study the authors provide a new high-quality non-anemonefish genome, which will be of high relevance to further the depth of such analyses. In this case of the sapphire damselfish Chrysiptera cyanea, a widely distributed damselfish in the Indo-Pacific area, often studied to elucidate the roles of various environmental controls on their reproduction, and investigate related hormonal processes To further the potential of biomolecular analyses based on this species, this study generated the first genome of a Chrysiptera fish from a male individual collected in Okinawa, Japan. Using PacBio and HiFI long-read sequencing with 94.5x coverage, a chromosome-scale genome was assembled and 28,173 genes identified and annotated. Peer review gathered more parameters and details on the quality, and the final assembly comprised of 896 Mb pairs across 91 contigs, and a BUSCO completeness of 97.6%. This reference genome should therefore be of high value for future genetic-based approaches, from population structure to gene expression analyses.
  

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

NeuroVar: an open-source tool for the visualization of gene expression and variation data for biomarkers of neurological diseases

1. Hiba Ben Aribi
2. Najla Abassi
3. Olaitan I. Awe

Reviewed by GigaByte

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

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

• 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

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

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

• 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

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

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

• 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

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

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

• 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

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

1. Saurabh Gupta
2. Ankur Sharma

• 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

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

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