VALOR2: Characterization of Large-scale Structural Variants Using Linked-reads

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2020 Mar 21

PMID 32192518

Citations 11

Authors

Fatih Karaoglanoglu

Camir Ricketts

Ezgi Ebren

Marzieh Eslami Rasekh

Iman Hajirasouliha

Can Alkan

Affiliations

Soon will be listed here.

Abstract

Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic segments, for example, inversions and translocations, is a particularly challenging task. Furthermore, there are very few algorithms to predict the insertion locus of large interspersed segmental duplications and characterize translocations. Here, we propose novel algorithms to characterize large interspersed segmental duplications, inversions, deletions, and translocations using linked-read sequencing data. We redesign our earlier algorithm, VALOR, and implement our new algorithms in a new software package, called VALOR2.

Citing Articles

Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.

Foltz S, Li Y, Yao L, Terekhanova N, Weerasinghe A, Gao Q bioRxiv. 2024; .

PMID: 39149342 PMC: 11326269. DOI: 10.1101/2024.08.09.607342.

The Bioinformatic Applications of Hi-C and Linked Reads.

Jiang L, Quail M, Fraser-Govil J, Wang H, Shi X, Oliver K Genomics Proteomics Bioinformatics. 2024; 22(4).

PMID: 38905513 PMC: 11580686. DOI: 10.1093/gpbjnl/qzae048.

LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.

Yang C, Zhang Z, Huang Y, Xie X, Liao H, Xiao J Gigascience. 2024; 13.

PMID: 38869148 PMC: 11170215. DOI: 10.1093/gigascience/giae028.

BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.

Hojer P, Frick T, Siga H, Pourbozorgi P, Aghelpasand H, Martin M Nucleic Acids Res. 2023; 51(22):e114.

PMID: 37941142 PMC: 10711428. DOI: 10.1093/nar/gkad1010.

MTG-Link: leveraging barcode information from linked-reads to assemble specific loci.

Guichard A, Legeai F, Tagu D, Lemaitre C BMC Bioinformatics. 2023; 24(1):284.

PMID: 37452278 PMC: 10347852. DOI: 10.1186/s12859-023-05395-w.

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