GigaByte (Hong Kong, China)最新文献

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

GigaByte (Hong Kong, China) Pub Date : 2025-03-07 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.152

Niema Moshiri

引用次数: 0

Portable-CELLxGENE: standalone executables of CELLxGENE for easy installation. Portable-CELLxGENE: CELLxGENE 的独立可执行文件，便于安装。

GigaByte (Hong Kong, China) Pub Date : 2025-03-03 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.151

George T Hall

{"title":"Portable-CELLxGENE: standalone executables of CELLxGENE for easy installation.","authors":"George T Hall","doi":"10.46471/gigabyte.151","DOIUrl":"10.46471/gigabyte.151","url":null,"abstract":"Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an intuitive graphical interface to facilitate analysis outside the command line, its server-side installation and execution remain complex. A version that is easier to install and run would allow non-bioinformaticians to take advantage of this valuable tool without needing to use the command line. This work introduces Portable-CELLxGENE, a standalone distribution of CELLxGENE that can be installed via a graphical interface. It contains an easy-to-use extension of the CELLxGENE-Gateway Python package to allow the analysis of multiple datasets. This tool enables non-bioinformaticians to carry out simple analyses independently.Availability and implementation: Versions of Portable-CELLxGENE for Windows and MacOS, along with source code, are available at https://george-hall-ucl.github.io/Portable-CELLxGENE-Docs. It is licensed under the GNU General Public License v3.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte151"},"PeriodicalIF":0.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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

GigaByte (Hong Kong, China) Pub Date : 2025-02-27 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.149

Eleanore J Ritter, Noé Cochetel, Andrea Minio, Peter Cousins, Dario Cantu, Chad Niederhuth

{"title":"The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired.","authors":"Eleanore J Ritter, Noé Cochetel, Andrea Minio, Peter Cousins, Dario Cantu, Chad Niederhuth","doi":"10.46471/gigabyte.149","DOIUrl":"10.46471/gigabyte.149","url":null,"abstract":"Teinturier grapevines, known for their pigmented flesh berries due to anthocyanin production, are valuable for enhancing the pigmentation of wine, for potential health benefits, and for investigating anthocyanin production in plants. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. For Dakapo, we combined Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine assembly to generate a final assembly of 508.5 Mbp. Combining de novo annotation and lifting over annotations from the existing grapevine reference produced annotation 36,940 gene annotations for Dakapo. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. De novo annotation of the diploid Rubired genome yielded annotations for 56,681 genes. Both genomes are highly contiguous and complete. The Dakapo and Rubired genome assemblies provide genetic resources for investigations into berry flesh pigmentation and other traits of interest in grapevine.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte149"},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143598414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species. 濒危的菲律宾特有物种鄢陵斑鹿（Rusa alfredi）的基因组草案。

GigaByte (Hong Kong, China) Pub Date : 2025-02-24 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.150

Ma Carmel F Javier, Albert C Noblezada, Persie Mark Q Sienes, Robert S Guino-O, Nadia Palomar-Abesamis, Maria Celia D Malay, Carmelo S Del Castillo, Victor Marco Emmanuel N Ferriols

{"title":"Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species.","authors":"Ma Carmel F Javier, Albert C Noblezada, Persie Mark Q Sienes, Robert S Guino-O, Nadia Palomar-Abesamis, Maria Celia D Malay, Carmelo S Del Castillo, Victor Marco Emmanuel N Ferriols","doi":"10.46471/gigabyte.150","DOIUrl":"10.46471/gigabyte.150","url":null,"abstract":"The Visayan Spotted Deer (VSD), or Rusa alfredi, is an endangered and endemic species in the Philippines. Despite its status, genomic information on R. alfredi, and the genus Rusa in general, is missing. This study presents the first draft genome assembly of the VSD using the Illumina short-read sequencing technology. The resulting RusAlf_1.1 assembly has a 2.52 Gb total length, with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genome's completeness, and includes the annotation of 24,531 genes. Our phylogenetic analysis based on single-copy orthologs revealed a close evolutionary relationship between R. alfredi and the genus Cervus. RusAlf_1.1 represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, potentially contributing to more effective conservation and management strategies for this endangered species.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte150"},"PeriodicalIF":0.0,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SqueezeCall: nanopore basecalling using a Squeezeformer network.

GigaByte (Hong Kong, China) Pub Date : 2025-02-14 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.148

Zhongxu Zhu

{"title":"SqueezeCall: nanopore basecalling using a Squeezeformer network.","authors":"Zhongxu Zhu","doi":"10.46471/gigabyte.148","DOIUrl":"10.46471/gigabyte.148","url":null,"abstract":"Nanopore sequencing, a third-generation sequencing technique, enables direct RNA sequencing, real-time analysis, and long-read length. Nanopore sequencers measure electrical current changes as nucleotides pass through nanopores; a basecaller identifies base sequences according to the raw current measurements. However, accurate basecalling remains challenging due to molecular variations and sequencing noise. Here, we introduce SqueezeCall, a novel Squeezeformer-based model for accurate nanopore basecalling. SqueezeCall uses convolution layers to down-sample raw signals and model local dependencies. A Squeezeformer network captures the global context, and a connectionist temporal classification (CTC) decoder with beam search generates DNA sequences. Experimental results demonstrated SqueezeCall's ability to resist noise, improving basecalling accuracy. We trained SqueezeCall combining three types of loss, and found that all three loss types contribute to basecalling accuracy. Experiments across multiple species demonstrated the potential of a Squeezeformer-based model to improve basecalling accuracy and its superiority over recurrent neural network-based models and Transformer-based models.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte148"},"PeriodicalIF":0.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11851125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143506532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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

GigaByte (Hong Kong, China) Pub Date : 2025-01-24 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.147

Deruilin Liu, Demin Xu, Liuxin Shi, Jiayuan Zhang, Kewei Bi, Bei Luo, Chen Liu, Yuxiang Li, Guangyi Fan, Wen Wang, Zhi Ping

{"title":"A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine.","authors":"Deruilin Liu, Demin Xu, Liuxin Shi, Jiayuan Zhang, Kewei Bi, Bei Luo, Chen Liu, Yuxiang Li, Guangyi Fan, Wen Wang, Zhi Ping","doi":"10.46471/gigabyte.147","DOIUrl":"10.46471/gigabyte.147","url":null,"abstract":"The DNA molecule is a promising next-generation data storage medium. Recently, it has been theoretically proposed that non-natural or modified bases can serve as extra molecular letters to increase the information density. However, this strategy is challenging due to the difficulty in synthesizing non-natural DNA sequences and their complex structure. Here, we described a practical DNA data storage transcoding scheme named R+ based on an expanded molecular alphabet that introduces 5-methylcytosine (5mC). We demonstrated its experimental validation by encoding one representative file into several 1.3∼1.6 kbps in vitro DNA fragments for nanopore sequencing. Our results show an average data recovery rate of 98.97% and 86.91% with and without reference, respectively. Our work validates the practicability of 5mC in DNA storage systems, with a potentially wide range of applications.Availability and implementation: R+ is implemented in Python and the code is available under a MIT license at https://github.com/Incpink-Liu/DNA-storage-R_plus.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte147"},"PeriodicalIF":0.0,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11791762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143191462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biodepot Launcher: an app to install, manage and launch bioinformatics workflows.

GigaByte (Hong Kong, China) Pub Date : 2025-01-14 eCollection Date: 2025-01-01 DOI: 10.46471/gigabyte.146

Ling-Hong Hung, Thomas J Dahlstrom, Johnalbert Garnica, Emmanuel Munoz, Robert Schmitz, Ka Yee Yeung

引用次数: 0

The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids. 蓝宝石雀鲷Chrysiptera cyanea的基因组：支持进一步研究Pomacentrids进化的新资源。

GigaByte (Hong Kong, China) Pub Date : 2024-12-31 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.144

Emma Gairin, Saori Miura, Hiroki Takamiyagi, Marcela Herrera, Vincent Laudet

{"title":"The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids.","authors":"Emma Gairin, Saori Miura, Hiroki Takamiyagi, Marcela Herrera, Vincent Laudet","doi":"10.46471/gigabyte.144","DOIUrl":"10.46471/gigabyte.144","url":null,"abstract":"The number of high-quality genomes is rapidly increasing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus Chrysiptera. Using PacBio long-read sequencing with 94.5× coverage, the genome of the Sapphire Devil, Chrysiptera cyanea, was assembled and annotated. The final assembly comprises 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%, and 28,173 genes. Comparative analyses with chromosome-scale assemblies of related species identified contig-chromosome correspondences. This genome will be useful as a comparison to study specific adaptations linked to the symbiotic life of closely related anemonefish. Furthermore, C. cyanea is found in most tropical coastal areas of the Indo-West Pacific and could become a model for environmental monitoring. This work will expand coral reef research efforts, highlighting the power of long-read assemblies to retrieve high quality genomes.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte144"},"PeriodicalIF":0.0,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11711634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Polyploid genome assembly of Cardamine chenopodiifolia. 小豆蔻的多倍体基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2024-12-23 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.145

Aurélia Emonet, Mohamed Awad, Nikita Tikhomirov, Maria Vasilarou, Miguel Pérez-Antón, Xiangchao Gan, Polina Yu Novikova, Angela Hay

{"title":"Polyploid genome assembly of Cardamine chenopodiifolia.","authors":"Aurélia Emonet, Mohamed Awad, Nikita Tikhomirov, Maria Vasilarou, Miguel Pérez-Antón, Xiangchao Gan, Polina Yu Novikova, Angela Hay","doi":"10.46471/gigabyte.145","DOIUrl":"10.46471/gigabyte.145","url":null,"abstract":"Cardamine chenopodiifolia is an amphicarpic plant in the Brassicaceae family. Plants develop two fruit types, one above and another below ground. This rare trait is associated with octoploidy in C. chenopodiifolia. The absence of genomic data for C. chenopodiifolia currently limits our understanding of the development and evolution of amphicarpy. Here, we produced a chromosome-scale assembly of the C. chenopodiifolia genome using high-fidelity long read sequencing with the Pacific Biosciences platform. We assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mb and an N50 of 18.8 Mb. Genome completeness was estimated at 99.8%. We observed structural variation among homeologous chromosomes, suggesting that C. chenopodiifolia originated via allopolyploidy, and phased the octoploid genome into four sub-genomes using orthogroup trees. This fully phased, chromosome-level genome assembly is an important resource to help investigate amphicarpy in C. chenopodiifolia and the origin of trait novelties by allopolyploidy.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte145"},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NeuroVar: an open-source tool for the visualization of gene expression and variation data for biomarkers of neurological diseases. NeuroVar：一个用于神经系统疾病生物标志物的基因表达和变异数据可视化的开源工具。

GigaByte (Hong Kong, China) Pub Date : 2024-11-25 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.143

Hiba Ben Aribi, Najla Abassi, Olaitan I Awe

引用次数: 0