GigaByte (Hong Kong, China)最新文献_第3页

CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa. CannSeek？是的，我们可以！针对大麻的开源单核苷酸多态性数据库和分析门户网站。

GigaByte (Hong Kong, China) Pub Date : 2024-10-08 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.135

Locedie Mansueto, Kenneth L McNally, Tobias Kretzschmar, Ramil Mauleon

{"title":"CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa.","authors":"Locedie Mansueto, Kenneth L McNally, Tobias Kretzschmar, Ramil Mauleon","doi":"10.46471/gigabyte.135","DOIUrl":"https://doi.org/10.46471/gigabyte.135","url":null,"abstract":"A growing interest in Cannabis sativa uses for food, fiber, and medicine, and recent changes in regulations have spurred numerous genomic studies of this once-prohibited plant. Cannabis research uses Next Generation Sequencing technologies for genomics and transcriptomics. While other crops have genome portals enabling access and analysis of numerous genotyping data from diverse accessions, leading to the discovery of alleles for important traits, this is absent for cannabis. The CannSeek web portal aims to address this gap. Single nucleotide polymorphism datasets were generated by identifying genome variants from public resequencing data and genome assemblies. Results and accompanying trait data are hosted in the CannSeek web application, built using the Rice SNP-Seek infrastructure with improvements to allow multiple reference genomes and provide a web-service Application Programming Interface. The tools built into the portal allow phylogenetic analyses, varietal grouping and identifications, and favorable haplotype discovery for cannabis accessions using public sequencing data.Availability and implementation: The CannSeek portal is available at https://icgrc.info/cannseek, https://icgrc.info/genotype_viewer.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte135"},"PeriodicalIF":0.0,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482386","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

High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome. 对一只惠比特犬进行高速全基因组测序：对速度极快的狗的基因组进行染色体级快速组装和注释。

GigaByte (Hong Kong, China) Pub Date : 2024-09-13 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.134

Marcel Nebenführ, David Prochotta, Alexander Ben Hamadou, Axel Janke, Charlotte Gerheim, Christian Betz, Carola Greve, Hanno Jörn Bolz

{"title":"High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome.","authors":"Marcel Nebenführ, David Prochotta, Alexander Ben Hamadou, Axel Janke, Charlotte Gerheim, Christian Betz, Carola Greve, Hanno Jörn Bolz","doi":"10.46471/gigabyte.134","DOIUrl":"10.46471/gigabyte.134","url":null,"abstract":"The time required for genome sequencing and de novo assembly depends on the interaction between laboratory work, sequencing capacity, and the bioinformatics workflow, often constrained by external sequencing services. Bringing together academic biodiversity institutes and a medical diagnostics company with extensive sequencing capabilities, we aimed at generating a high-quality mammalian de novo genome in minimal time. We present the first chromosome-level genome assembly of the Whippet, using PacBio long-read high-fidelity sequencing and reference-guided scaffolding. The final assembly has a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. The total assembly length is 2.47 Gbp, of which 2.43 Gpb were scaffolded into 39 chromosome-length scaffolds. Annotation using mammalian genomes and transcriptome data yielded 28,383 transcripts, 90.9% complete BUSCO genes, and identified 36.5% repeat content. Sequencing, assembling, and scaffolding the chromosome-level genome of the Whippet took less than a week, adding another high-quality reference genome to the available sequences of domestic dog breeds.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte134"},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11418881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309262","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

RiboSnake - a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis. RiboSnake - 用于 16S rRNA 基因微生物组分析的用户友好型、稳健型、可重现型、多用途和文档丰富型管道。

GigaByte (Hong Kong, China) Pub Date : 2024-08-31 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.132

Ann-Kathrin Dörr, Josefa Welling, Adrian Dörr, Jule Gosch, Hannah Möhlen, Ricarda Schmithausen, Jan Kehrmann, Folker Meyer, Ivana Kraiselburd

{"title":"RiboSnake - a user-friendly, robust, reproducible, multipurpose and documentation-extensive pipeline for 16S rRNA gene microbiome analysis.","authors":"Ann-Kathrin Dörr, Josefa Welling, Adrian Dörr, Jule Gosch, Hannah Möhlen, Ricarda Schmithausen, Jan Kehrmann, Folker Meyer, Ivana Kraiselburd","doi":"10.46471/gigabyte.132","DOIUrl":"10.46471/gigabyte.132","url":null,"abstract":"Background: Next-generation sequencing for microbial communities has become a standard technique. However, the computational analysis remains resource-intensive. With declining costs and growing adoption of sequencing-based methods in many fields, validated, fully automated, reproducible and flexible pipelines are increasingly essential in various scientific fields.Results: We present RiboSnake, a validated, automated, reproducible QIIME2-based pipeline implemented in Snakemake for analysing 16S rRNA gene amplicon sequencing data. RiboSnake includes pre-packaged validated parameter sets optimized for different sample types, from environmental samples to patient data. The configuration packages can be easily adapted and shared, requiring minimal user input.Conclusion: RiboSnake is a new alternative for researchers employing 16S rRNA gene amplicon sequencing and looking for a customizable and user-friendly pipeline for microbiome analyses with in vitro validated settings. By automating the analysis with validated parameters for diverse sample types, RiboSnake enhances existing methods significantly. The workflow repository can be found on GitHub (https://github.com/IKIM-Essen/RiboSnake).","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte132"},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11448241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373717","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

Automated management of AWS instances for training. 自动管理用于培训的 AWS 实例。

GigaByte (Hong Kong, China) Pub Date : 2024-08-29 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.133

Jorge Buenabad-Chavez, Evelyn Greeves, James P J Chong, Emma Rand

引用次数: 0

Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor. 黑脸琵鹭（Platalea minor）的染色体级基因组组装和单核苷酸多态性位点。

GigaByte (Hong Kong, China) Pub Date : 2024-07-18 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.130

引用次数: 0

Kinship analysis and pedigree reconstruction by RAD sequencing in cattle. 通过 RAD 测序对牛进行亲缘关系分析和血统重建。

GigaByte (Hong Kong, China) Pub Date : 2024-07-18 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.131

Yiming Xu, Wanqiu Wang, Jiefeng Huang, Minjie Xu, Binhu Wang, Yingsong Wu, Yongzhong Xie, Jianbo Jian

{"title":"Kinship analysis and pedigree reconstruction by RAD sequencing in cattle.","authors":"Yiming Xu, Wanqiu Wang, Jiefeng Huang, Minjie Xu, Binhu Wang, Yingsong Wu, Yongzhong Xie, Jianbo Jian","doi":"10.46471/gigabyte.131","DOIUrl":"10.46471/gigabyte.131","url":null,"abstract":"Kinship and pedigree, used for estimating inbreeding, heritability, selection, and gene flow, are useful for breeding and animal conservation. However, as the size of crossbred populations increases, inaccurate generation and parentage assignment in livestock farms increase. Restriction-site-associated DNA sequencing is a cost-effective platform for single nucleotide polymorphism (SNP) discovery and genotyping. Here, we performed a kinship analysis and pedigree reconstruction for 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. The identified SNP panel included 7,305 SNPs capturing the maximum difference between paternal and maternal genome information, allowing us to distinguish F1 from F2 generations with 90% accuracy. In conclusion, we provided a low-cost and efficient SNP panel for kinship analyses and the improvement of local genetic resources, which are valuable for breed improvement, local resource utilization, and conservation.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11273509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141790212","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

Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients. 为高度选择性的严重 COVID-19 患者队列进行低覆盖率全基因组测序。

GigaByte (Hong Kong, China) Pub Date : 2024-06-20 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.127

Renato Santos, Víctor Moreno-Torres, Ilduara Pintos, Octavio Corral, Carmen de Mendoza, Vicente Soriano, Manuel Corpas

{"title":"Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patients.","authors":"Renato Santos, Víctor Moreno-Torres, Ilduara Pintos, Octavio Corral, Carmen de Mendoza, Vicente Soriano, Manuel Corpas","doi":"10.46471/gigabyte.127","DOIUrl":"10.46471/gigabyte.127","url":null,"abstract":"Despite the advances in genetic marker identification associated with severe COVID-19, the full genetic characterisation of the disease remains elusive. This study explores imputation in low-coverage whole genome sequencing for a severe COVID-19 patient cohort. We generated a dataset of 79 imputed variant call format files using the GLIMPSE1 tool, each containing an average of 9.5 million single nucleotide variants. Validation revealed a high imputation accuracy (squared Pearson correlation ≍0.97) across sequencing platforms, showcasing GLIMPSE1's ability to confidently impute variants with minor allele frequencies as low as 2% in individuals with Spanish ancestry. We carried out a comprehensive analysis of the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms developed to characterise severe COVID-19 symptoms. The methods and findings presented here can be leveraged for future genomic projects to gain vital insights into health challenges like COVID-19.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte127"},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473253","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

PhysiCell Studio: a graphical tool to make agent-based modeling more accessible. PhysiCell Studio：一种使基于代理的建模更易于使用的图形工具。

GigaByte (Hong Kong, China) Pub Date : 2024-06-19 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.128

Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow, Julie Cass, Heber Lima da Rocha, Marco Ruscone, Vincent Noël, Paul Macklin

{"title":"PhysiCell Studio: a graphical tool to make agent-based modeling more accessible.","authors":"Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow, Julie Cass, Heber Lima da Rocha, Marco Ruscone, Vincent Noël, Paul Macklin","doi":"10.46471/gigabyte.128","DOIUrl":"10.46471/gigabyte.128","url":null,"abstract":"Defining a multicellular model can be challenging. There may be hundreds of parameters that specify the attributes and behaviors of objects. In the best case, the model will be defined using some format specification - a markup language - that will provide easy model sharing (and a minimal step toward reproducibility). PhysiCell is an open-source, physics-based multicellular simulation framework with an active and growing user community. It uses XML to define a model and, traditionally, users needed to manually edit the XML to modify the model. PhysiCell Studio is a tool to make this task easier. It provides a GUI that allows editing the XML model definition, including the creation and deletion of fundamental objects: cell types and substrates in the microenvironment. It also lets users build their model by defining initial conditions and biological rules, run simulations, and view results interactively. PhysiCell Studio has evolved over multiple workshops and academic courses in recent years, which has led to many improvements. There is both a desktop and cloud version. Its design and development has benefited from an active undergraduate and graduate research program. Like PhysiCell, the Studio is open-source software and contributions from the community are encouraged.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2024 ","pages":"gigabyte128"},"PeriodicalIF":0.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473254","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

Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis. 用于纳米孔直接 RNA 分析的多细胞、IVT 衍生、未修饰的人类转录组。

GigaByte (Hong Kong, China) Pub Date : 2024-06-17 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.129

Caroline A McCormick, Stuart Akeson, Sepideh Tavakoli, Dylan Bloch, Isabel N Klink, Miten Jain, Sara H Rouhanifard

引用次数: 0

Get Free Copy: a multi-repository search platform for biomedical publications. 免费获取副本：生物医学出版物的多库检索平台。

GigaByte (Hong Kong, China) Pub Date : 2024-05-29 eCollection Date: 2024-01-01 DOI: 10.46471/gigabyte.126

Nodir Kosimkhujaev, Kuan-Lin Huang

引用次数: 0