GigaByte (Hong Kong, China)最新文献_第7页

A database of restriction maps to expand the utility of bacterial artificial chromosomes. 一个限制性图谱数据库，以扩大细菌人工染色体的实用性。

GigaByte (Hong Kong, China) Pub Date : 2023-09-20 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.93

Eamon Winden, Alejandro Vasquez-Echeverri, Susana Calle-Castañeda, Yumin Lian, Juan Pablo Hernandez Ortiz, David C Schwartz

引用次数: 0

ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R. ensemblQueryR：在R中对Ensembl LD API端点进行快速、灵活、高吞吐量的查询。

GigaByte (Hong Kong, China) Pub Date : 2023-09-14 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.91

Aine Fairbrother-Browne, Sonia García-Ruiz, Regina Hertfelder Reynolds, Mina Ryten, Alan Hodgkinson

{"title":"ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R.","authors":"Aine Fairbrother-Browne, Sonia García-Ruiz, Regina Hertfelder Reynolds, Mina Ryten, Alan Hodgkinson","doi":"10.46471/gigabyte.91","DOIUrl":"10.46471/gigabyte.91","url":null,"abstract":"We present ensemblQueryR, an R package for querying Ensembl linkage disequilibrium (LD) endpoints. This package is flexible, fast and user-friendly, and optimised for high-throughput querying. ensemblQueryR uses functions that are intuitive and amenable to custom code integration, familiar R object types as inputs and outputs as well as providing parallelisation functionality. For each Ensembl LD endpoint, ensemblQueryR provides two functions, permitting both single- and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate improved computational performance of ensemblQueryR over an exisiting tool in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through Docker and singularity images, making this tool widely accessible to the scientific community.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10507293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41153439","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

Genome assembly and annotation of the Sharp-nosed Pit Viper Deinagkistrodon acutus based on next-generation sequencing data. 基于新一代测序数据的尖吻蝮基因组组装和注释。

GigaByte (Hong Kong, China) Pub Date : 2023-09-04 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.88

Xinyu Wang, Lirong Liu, Wenbiao Zhu, Shiqing Wang, Minhui Shi, Shuhui Yang, Haorong Lu, Jun Cao

引用次数: 0

Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies. 小号图：可视化遗传关联研究中等位基因频率与效应大小之间的关系。

GigaByte (Hong Kong, China) Pub Date : 2023-09-01 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.89

Lucia Corte, Lathan Liou, Paul F O'Reilly, Judit García-González

{"title":"Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies.","authors":"Lucia Corte, Lathan Liou, Paul F O'Reilly, Judit García-González","doi":"10.46471/gigabyte.89","DOIUrl":"10.46471/gigabyte.89","url":null,"abstract":"Recent advances in genome-wide association and sequencing studies have shown that the genetic architecture of complex traits and diseases involves a combination of rare and common genetic variants distributed throughout the genome. One way to better understand this architecture is to visualize genetic associations across a wide range of allele frequencies. However, there is currently no standardized or consistent graphical representation for effectively illustrating these results. Here we propose a standardized approach for visualizing the effect size of risk variants across the allele frequency spectrum. The proposed plots have a distinctive trumpet shape: with the majority of variants having high frequency and small effects, and a small number of variants having lower frequency and larger effects. To demonstrate the utility of trumpet plots in illustrating the relationship between the number of variants, their frequency, and the magnitude of their effects in shaping the genetic architecture of complex traits and diseases, we generated trumpet plots for more than one hundred traits in the UK Biobank. To facilitate their broader use, we developed an R package, 'TrumpetPlots' (available at the Comprehensive R Archive Network) and R Shiny application, 'Shiny Trumpets' (available at https://juditgg.shinyapps.io/shinytrumpets/) that allows users to explore these results and submit their own data.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte89"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10268544","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

aws-s3-integrity-check: an open-source bash tool to verify the integrity of a dataset stored on Amazon S3. aws-s3-integrity-check：一款开源 bash 工具，用于验证存储在亚马逊 S3 上的数据集的完整性。

GigaByte (Hong Kong, China) Pub Date : 2023-08-23 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.87

Sonia García-Ruiz, Regina Hertfelder Reynolds, Melissa Grant-Peters, Emil Karl Gustavsson, Aine Fairbrother-Browne, Zhongbo Chen, Jonathan William Brenton, Mina Ryten

{"title":"aws-s3-integrity-check: an open-source bash tool to verify the integrity of a dataset stored on Amazon S3.","authors":"Sonia García-Ruiz, Regina Hertfelder Reynolds, Melissa Grant-Peters, Emil Karl Gustavsson, Aine Fairbrother-Browne, Zhongbo Chen, Jonathan William Brenton, Mina Ryten","doi":"10.46471/gigabyte.87","DOIUrl":"10.46471/gigabyte.87","url":null,"abstract":"Amazon Simple Storage Service (Amazon S3) is a widely used platform for storing large biomedical datasets. Unintended data alterations can occur during data writing and transmission, altering the original content and generating unexpected results. However, no open-source and easy-to-use tool exists to verify end-to-end data integrity. Here, we present aws-s3-integrity-check, a user-friendly, lightweight, and reliable bash tool to verify the integrity of a dataset stored in an Amazon S3 bucket. Using this tool, we only needed ∼114 min to verify the integrity of 1,045 records ranging between 5 bytes and 10 gigabytes and occupying ∼935 gigabytes of the Amazon S3 cloud. Our aws-s3-integrity-check tool also provides file-by-file on-screen and log-file-based information about the status of each integrity check. To our knowledge, this tool is the only open-source one that allows verifying the integrity of a dataset uploaded to the Amazon S3 Storage quickly, reliably, and efficiently. The tool is freely available for download and use at https://github.com/SoniaRuiz/aws-s3-integrity-check and https://hub.docker.com/r/soniaruiz/aws-s3-integrity-check.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte87"},"PeriodicalIF":0.0,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10448181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10165035","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 dataset and template for assessing the ecological status of marine sediments and waters, based on microbial taxa. 根据微生物类群评估海洋沉积物和水域生态状况的数据集和模板。

GigaByte (Hong Kong, China) Pub Date : 2023-08-14 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.86

Angel Borja

引用次数: 0

Digitizing the Culicidae collection of Naturalis Biodiversity Center, with a special focus on the former Bonne-Wepster subcollection. 将纳洛利斯生物多样性中心的蝇科动物藏品数字化，特别关注前 Bonne-Wepster 子藏品。

GigaByte (Hong Kong, China) Pub Date : 2023-07-18 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.85

Pasquale Ciliberti, Astrid Roquas, Becky Desjardins, Bibiche Berkholst, Frank Loggen, Menno Hooft, Gideon Gijswijt, Dick de Graaff

{"title":"Digitizing the Culicidae collection of Naturalis Biodiversity Center, with a special focus on the former Bonne-Wepster subcollection.","authors":"Pasquale Ciliberti, Astrid Roquas, Becky Desjardins, Bibiche Berkholst, Frank Loggen, Menno Hooft, Gideon Gijswijt, Dick de Graaff","doi":"10.46471/gigabyte.85","DOIUrl":"10.46471/gigabyte.85","url":null,"abstract":"Natural history collections contain a wealth of information on species diversity, distribution and ecology. However, due to historical and practical constraints, this valuable information is not always available to researchers. Our project aimed at unlocking data handwritten in notebooks owned by Johanna Bonne-Wepster, a Culicidae researcher. These handwritten notes refer to specimens labeled with a number only. The notebooks were scanned and entered into a Google spreadsheet. The specimens were provided with a unique identifier, labeled with the information from the notebooks and the data exported to the Global Biodiversity Information Facility. In addition, the type specimens were photographed. Besides Johanna Bonne-Wepster's collection, mosquitoes from the former Rijksmuseum van Natuurlijk Historie collection and the former Zoölogisch Museum Amsterdam Nederland collection were digitized. All specimens are now housed at the Naturalis Biodiversity Center museum in Leiden. This paper describes the efforts to mobilize this data and the problems we encountered.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte85"},"PeriodicalIF":0.0,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10355122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10208256","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

Genome assembly of the hybrid grapevine Vitis 'Chambourcin'. 杂交葡萄藤'Chambourcin'的基因组组装。

GigaByte (Hong Kong, China) Pub Date : 2023-07-03 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.84

Sagar Patel, Zachary N Harris, Jason P Londo, Allison Miller, Anne Fennell

引用次数: 0

Anopheles sampling collections in the health districts of Korhogo (Côte d'Ivoire) and Diébougou (Burkina Faso) between 2016 and 2018. 2016 年至 2018 年期间在科霍戈（科特迪瓦）和迪布古（布基纳法索）卫生区采集的疟蚊样本。

GigaByte (Hong Kong, China) Pub Date : 2023-06-30 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.83

Paul Taconet, Barnabas Zogo, Dieudonné Diloma Soma, Ludovic P Ahoua Alou, Karine Mouline, Roch Kounbobr Dabiré, Alphonsine Amanan Koffi, Cédric Pennetier, Nicolas Moiroux

{"title":"Anopheles sampling collections in the health districts of Korhogo (Côte d'Ivoire) and Diébougou (Burkina Faso) between 2016 and 2018.","authors":"Paul Taconet, Barnabas Zogo, Dieudonné Diloma Soma, Ludovic P Ahoua Alou, Karine Mouline, Roch Kounbobr Dabiré, Alphonsine Amanan Koffi, Cédric Pennetier, Nicolas Moiroux","doi":"10.46471/gigabyte.83","DOIUrl":"10.46471/gigabyte.83","url":null,"abstract":"Characterizing the entomological profile of malaria transmission at fine spatiotemporal scales is essential for developing and implementing effective vector control strategies. Here, we present a fine-grained dataset of Anopheles mosquitoes (Diptera: Culicidae) collected in 55 villages of the rural districts of Korhogo (Northern Côte d'Ivoire) and Diébougou (South-West Burkina Faso) between 2016 and 2018. In the framework of a randomized controlled trial, Anopheles mosquitoes were periodically collected by Human Landing Catches experts inside and outside households, and analyzed individually to identify the genus and, for a subsample, species, insecticide resistance genetic mutations, Plasmodium falciparum infection, and parity status. More than 3,000 collection sessions were carried out, achieving about 45,000 h of sampling efforts. Over 60,000 Anopheles were collected (mainly A. gambiae s.s., A. coluzzii, and A. funestus). The dataset is published as a Darwin Core archive in the Global Biodiversity Information Facility, comprising four files: events, occurrences, mosquito characterizations, and environmental data.","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2023 ","pages":"gigabyte83"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10318348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9803417","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 genome assembly and annotation of the many-banded krait, Bungarus multicinctus. 多带石龙子（Bungarus multicinctus）的基因组组装和注释。

GigaByte (Hong Kong, China) Pub Date : 2023-06-29 eCollection Date: 2023-01-01 DOI: 10.46471/gigabyte.82

Boyang Liu, Liangyu Cui, Zhangwen Deng, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Tianming Lan, Shuhui Yang, Song Huang

引用次数: 0