Tag: SV

LinkedSV – SV Detection on linked-read Sequencing data

LinkedSV

:: DESCRIPTION

LinkedSV is a novel structural variant caller for 10X Genomics (linked-read) sequencing data. It detects deletions, duplications, inversions and translocations using evidence from the barcoded reads.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

LinkedSV

:: MORE INFORMATION

Citation

Fang L, Kao C, Gonzalez MV, Mafra FA, Pellegrino da Silva R, Li M, Wenzel SS, Wimmer K, Hakonarson H, Wang K.
LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data.
Nat Commun. 2019 Dec 6;10(1):5585. doi: 10.1038/s41467-019-13397-7. PMID: 31811119; PMCID: PMC6898185.

SoftSearch 1.0 – Structural Variant (SV) Detection tool

SoftSearch 1.0

:: DESCRIPTION

SoftSearch is a sensitive structural variant detection (SV) detection tool for Illumina paired-end next-generation sequencing data. SoftSearch simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SoftSearch

:: MORE INFORMATION

Citation

PLoS One. 2013 Dec 16;8(12):e83356. doi: 10.1371/journal.pone.0083356. eCollection 2013.
SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.
Hart SN1, Sarangi V1, Moore R1, Baheti S1, Bhavsar JD1, Couch FJ2, Kocher JP