TRTools：用于串联重复序列全基因组分析的工具包。
TRTools: a toolkit for genome-wide analysis of tandem repeats.
机构信息
Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, 92093, USA.
Department of Medicine, University of California San Diego, La Jolla, 92093, USA.
出版信息
Bioinformatics. 2021 May 5;37(5):731-733. doi: 10.1093/bioinformatics/btaa736.
Abstract
SUMMARY
A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.
AVAILABILITY AND IMPLEMENTATION
TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
摘要
最近开发了一套丰富的工具，用于进行串联重复（TR）的全基因组基因分型。然而，缺乏对这些结果进行下游分析的标准化工具。为了促进 TR 分析应用，我们提出了 TRTools，这是一个用于过滤、合并和 TR 基因型文件质量控制的 Python 库和命令行工具套件。TRTools 利用内部协调模块，使其与各种 TR 基因分型器的输出兼容。
可用性和实现
TRTools 可在 https://github.com/gymreklab/TRTools 上免费获得。详细文档可在 https://trtools.readthedocs.io 上获得。
补充信息
补充数据可在生物信息学在线获得。
相似文献
1
TRTools: a toolkit for genome-wide analysis of tandem repeats.TRTools：用于串联重复序列全基因组分析的工具包。
Bioinformatics. 2021 May 5;37(5):731-733. doi: 10.1093/bioinformatics/btaa736.
2
TRviz: a Python library for decomposing and visualizing tandem repeat sequences.TRviz：一个用于分解和可视化串联重复序列的Python库。
Bioinform Adv. 2023 Apr 26;3(1):vbad058. doi: 10.1093/bioadv/vbad058. eCollection 2023.
3
Genome-wide detection of somatic mosaicism at short tandem repeats.全基因组范围内短串联重复序列的体细胞嵌合现象检测。
bioRxiv. 2023 Nov 23:2023.11.22.568371. doi: 10.1101/2023.11.22.568371.
4
Genome-wide detection of somatic mosaicism at short tandem repeats.全基因组范围内短串联重复序列的体细胞镶嵌性检测。
Bioinformatics. 2024 Aug 2;40(8). doi: 10.1093/bioinformatics/btae485.
5
Haptools: a toolkit for admixture and haplotype analysis.Haptools：混合分析和单倍型分析工具包。
Bioinformatics. 2023 Mar 1;39(3). doi: 10.1093/bioinformatics/btad104.
6
SquiggleKit: a toolkit for manipulating nanopore signal data.SquiggleKit：用于处理纳米孔信号数据的工具包。
Bioinformatics. 2019 Dec 15;35(24):5372-5373. doi: 10.1093/bioinformatics/btz586.
7
HOMELETTE: a unified interface to homology modelling software.HOMELETTE：同源建模软件的统一接口。
Bioinformatics. 2022 Mar 4;38(6):1749-1751. doi: 10.1093/bioinformatics/btab866.
8
genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.Genipe：一个具有自动报告和统计工具的全基因组自动化插补流程。
Bioinformatics. 2016 Dec 1;32(23):3661-3663. doi: 10.1093/bioinformatics/btw487. Epub 2016 Aug 6.
9
ipyrad: Interactive assembly and analysis of RADseq datasets.ipyrad：RADseq 数据集的交互式组装和分析。
Bioinformatics. 2020 Apr 15;36(8):2592-2594. doi: 10.1093/bioinformatics/btz966.
10
GSEApy: a comprehensive package for performing gene set enrichment analysis in Python.GSEApy：一个用于在 Python 中进行基因集富集分析的综合软件包。
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac757.
引用本文的文献
1
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.利用多种工具的一致性基因型识别串联重复序列与复杂人类性状之间关联的实用指南。
Nat Protoc. 2025 Sep 1. doi: 10.1038/s41596-025-01231-y.
2
Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis.短串联重复序列的突变解释了拟南芥中丰富的性状遗传力。
Genome Biol. 2025 Aug 12;26(1):242. doi: 10.1186/s13059-025-03720-5.
3
An integrated framework for functional dissection of variable expressivity in genetic disorders.一种用于对遗传疾病中可变表达进行功能剖析的综合框架。
medRxiv. 2025 Jul 24:2025.07.22.25331885. doi: 10.1101/2025.07.22.25331885.
4
Enrichment of tandem repeat element variants near CHD genes identified by short- and long-read genome sequencing.通过短读长和长读长基因组测序鉴定的冠心病基因附近串联重复元件变异的富集。
BMC Med Genomics. 2025 Jul 25;18(1):120. doi: 10.1186/s12920-025-02191-8.
5
TRACKing tandem repeats: a customizable pipeline for identification and cross-species comparison.追踪串联重复序列：用于识别和跨物种比较的可定制流程
Bioinform Adv. 2025 Apr 8;5(1):vbaf066. doi: 10.1093/bioadv/vbaf066. eCollection 2025.
6
Polymorphic tandem repeats influence cell type-specific gene expression across the human immune landscape.多态性串联重复序列影响人类免疫图谱中细胞类型特异性基因表达。
bioRxiv. 2025 Apr 9:2024.11.02.621562. doi: 10.1101/2024.11.02.621562.
7
SatXplor-a comprehensive pipeline for satellite DNA analyses in complex genome assemblies.SatXplor——用于复杂基因组组装中卫星DNA分析的综合流程。
Brief Bioinform. 2024 Nov 22;26(1). doi: 10.1093/bib/bbae660.
8
Genetic modifiers and ascertainment drive variable expressivity of complex disorders.基因修饰因子与确诊因素导致复杂疾病的可变表达。
medRxiv. 2024 Aug 28:2024.08.27.24312158. doi: 10.1101/2024.08.27.24312158.
9
Y and mitochondrial chromosomes in the heterogeneous stock rat population.异质 stock 大鼠种群中的 Y 和线粒体染色体。
G3 (Bethesda). 2024 Nov 6;14(11). doi: 10.1093/g3journal/jkae213.
10
Genome-wide detection of somatic mosaicism at short tandem repeats.全基因组范围内短串联重复序列的体细胞镶嵌性检测。
Bioinformatics. 2024 Aug 2;40(8). doi: 10.1093/bioinformatics/btae485.
本文引用的文献
1
popSTR2 enables clinical and population-scale genotyping of microsatellites.popSTR2 可用于微卫星的临床和人群规模基因分型。
Bioinformatics. 2020 Apr 1;36(7):2269-2271. doi: 10.1093/bioinformatics/btz913.
2
Profiling the genome-wide landscape of tandem repeat expansions.全基因组串联重复扩展图谱分析。
Nucleic Acids Res. 2019 Sep 5;47(15):e90. doi: 10.1093/nar/gkz501.
3
Targeted genotyping of variable number tandem repeats with adVNTR.使用 adVNTR 进行可变数目串联重复序列的靶向基因分型。
Genome Res. 2018 Nov;28(11):1709-1719. doi: 10.1101/gr.235119.118. Epub 2018 Oct 23.
4
Tandem repeats mediating genetic plasticity in health and disease.串联重复序列介导健康与疾病中的遗传可塑性。
Nat Rev Genet. 2018 May;19(5):286-298. doi: 10.1038/nrg.2017.115. Epub 2018 Feb 5.
5
Detection of long repeat expansions from PCR-free whole-genome sequence data.从无 PCR 全基因组序列数据中检测长重复扩展。
Genome Res. 2017 Nov;27(11):1895-1903. doi: 10.1101/gr.225672.117. Epub 2017 Sep 8.
6
Genome-wide profiling of heritable and de novo STR variations.可遗传和新生STR变异的全基因组分析
Nat Methods. 2017 Jun;14(6):590-592. doi: 10.1038/nmeth.4267. Epub 2017 Apr 24.
7
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.一种用于从测序数据中进行 SNP 调用、突变发现、关联映射和群体遗传参数估计的统计框架。
Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. Epub 2011 Sep 8.
Zotero 插件