VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing

被引：27

作者：

Bolognini, Davide ^{[1
,2
]}

Sanders, Ashley ^{[3
]}

Korbel, Jan O. ^{[3
]}

Magi, Alberto ^{[4
]}

Benes, Vladimir ^{[2
]}

Rausch, Tobias ^{[2
,3
]}

机构：

[1] Univ Florence, Dept Expt & Clin Med, I-50134 Florence, Italy

[2] European Mol Biol Lab, GeneCore, D-69917 Heidelberg, Germany

[3] European Mol Biol Lab, Genome Biol Unit, D-69917 Heidelberg, Germany

[4] Univ Florence, Dept Informat Engn, I-50134 Florence, Italy

来源：

BIOINFORMATICS | 2020年 / 36卷 / 04期

基金：

欧洲研究理事会;

关键词：

STRAND-SEQ;

D O I：

10.1093/bioinformatics/btz719

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

VISOR is a tool for haplotype-specific simulations of simple and complex structural variants (SVs). The method is applicable to haploid, diploid or higher ploidy simulations for bulk or single-cell sequencing data. SVs are implanted into FASTA haplotypes at single-basepair resolution, optionally with nearby single-nucleotide variants. Short or long reads are drawn at random from these haplotypes using standard error profiles. Double- or single-stranded data can be simulated and VISOR supports the generation of haplotype-tagged BAM files. The tool further includes methods to interactively visualize simulated variants in single-stranded data. The versatility of VISOR is unmet by comparable tools and it lays the foundation to simulate haplotype-resolved cancer heterogeneity data in bulk or at single-cell resolution.

引用

页码：1267 / 1269

页数：3

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