BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata.

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
Linda Fenske, Lukas Jelonek, Alexander Goesmann, Oliver Schwengers
{"title":"BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata.","authors":"Linda Fenske, Lukas Jelonek, Alexander Goesmann, Oliver Schwengers","doi":"10.1099/mgen.0.001305","DOIUrl":null,"url":null,"abstract":"<p><p>Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding. Meanwhile, access to cost-effective sequencing platforms has accelerated bacterial WGS to unprecedented levels, introducing new challenges in terms of data accessibility, computational demands, heterogeneity of analysis workflows and, thus, ultimately its scientific usability. To this end, a previous study released a uniformly processed set of 661 405 bacterial genome assemblies obtained from the European Nucleotide Archive as of November 2018. Building on these accomplishments, we conducted further genome-based analyses like taxonomic classification, multilocus sequence typing and annotation of all genomes. Here, we present BakRep, a searchable large-scale web repository of these genomes enriched with consistent genome characterizations and original metadata. The platform provides a flexible search engine combining taxonomic, genomic and metadata information, as well as interactive elements to visualize genomic features. Furthermore, all results can be downloaded for offline analyses via an accompanying command line tool. The web repository is accessible via https://bakrep.computational.bio.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0000,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524574/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbial Genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1099/mgen.0.001305","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

Abstract

Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding. Meanwhile, access to cost-effective sequencing platforms has accelerated bacterial WGS to unprecedented levels, introducing new challenges in terms of data accessibility, computational demands, heterogeneity of analysis workflows and, thus, ultimately its scientific usability. To this end, a previous study released a uniformly processed set of 661 405 bacterial genome assemblies obtained from the European Nucleotide Archive as of November 2018. Building on these accomplishments, we conducted further genome-based analyses like taxonomic classification, multilocus sequence typing and annotation of all genomes. Here, we present BakRep, a searchable large-scale web repository of these genomes enriched with consistent genome characterizations and original metadata. The platform provides a flexible search engine combining taxonomic, genomic and metadata information, as well as interactive elements to visualize genomic features. Furthermore, all results can be downloaded for offline analyses via an accompanying command line tool. The web repository is accessible via https://bakrep.computational.bio.

BakRep - 可搜索的大规模细菌基因组、特征和元数据网络存储库。
细菌在许多学科中都是引人入胜的研究对象,原因不胜枚举,而全基因组测序(WGS)已成为促进我们对微生物了解的最重要方法。与此同时,高性价比测序平台的使用加速了细菌全基因组测序(WGS)的发展,使其达到了前所未有的水平,并在数据获取、计算需求、分析工作流程的异质性等方面带来了新的挑战,从而最终提高了其科学实用性。为此,之前的一项研究发布了截至 2018 年 11 月从欧洲核苷酸档案馆获得的经过统一处理的 661 405 个细菌基因组组装集。在这些成就的基础上,我们进一步开展了基于基因组的分析,如分类学分类、多焦点序列分型和所有基因组的注释。在此,我们介绍 BakRep,这是一个可搜索的大规模网络基因组库,其中丰富了一致的基因组特征和原始元数据。该平台提供了一个灵活的搜索引擎,结合了分类学、基因组和元数据信息,以及可视化基因组特征的互动元素。此外,所有结果都可以通过随附的命令行工具下载,进行离线分析。网络资源库可通过 https://bakrep.computational.bio 访问。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Microbial Genomics
Microbial Genomics Medicine-Epidemiology
CiteScore
6.60
自引率
2.60%
发文量
153
审稿时长
12 weeks
期刊介绍: Microbial Genomics (MGen) is a fully open access, mandatory open data and peer-reviewed journal publishing high-profile original research on archaea, bacteria, microbial eukaryotes and viruses.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信