Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2021-03-16 DOI:10.1186/s13059-021-02303-4
Huiguang Yi, Yanling Lin, Chengqi Lin, Wenfei Jin
{"title":"Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.","authors":"Huiguang Yi, Yanling Lin, Chengqi Lin, Wenfei Jin","doi":"10.1186/s13059-021-02303-4","DOIUrl":null,"url":null,"abstract":"<p><p>Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data. Using Kssd, we prioritize references for all 1,019,179 bacteria whole genome sequencing (WGS) runs from NCBI Sequence Read Archive and find misidentification or contamination in 6164 of these. Additionally, we analyze WGS and exome runs of samples from the 1000 Genomes Project.</p>","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"22 1","pages":"84"},"PeriodicalIF":12.3000,"publicationDate":"2021-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7962209/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-021-02303-4","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
引用次数: 0

Abstract

Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data. Using Kssd, we prioritize references for all 1,019,179 bacteria whole genome sequencing (WGS) runs from NCBI Sequence Read Archive and find misidentification or contamination in 6164 of these. Additionally, we analyze WGS and exome runs of samples from the 1000 Genomes Project.

Abstract Image

Abstract Image

Abstract Image

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Kssd:通过 k-mer 子串空间采样降低序列维度,实现实时大规模数据集分析。
在这里,我们开发了 k -mer 子串空间分解(Kssd),这是一种草图绘制技术,与当前的草图绘制方法相比,速度更快,精度更高。我们的研究表明,这是唯一一种可以在模拟数据和真实数据的群体分辨率下进行大规模数据集比较的方法。利用 Kssd,我们对 NCBI Sequence Read Archive 中所有 1,019,179 个细菌全基因组测序(WGS)运行的参考文献进行了优先排序,发现其中 6164 个存在识别错误或污染。此外,我们还分析了来自 1000 基因组计划的 WGS 和外显子组运行样本。
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 去求助
来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
期刊最新文献
Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion. DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates. Seqrutinator: scrutiny of large protein superfamily sequence datasets for the identification and elimination of non-functional homologues. Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. TaqTth-hpRNA: a novel compact RNA-targeting tool for specific silencing of pathogenic mRNA.
×
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
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 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 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1