Tag: Structural Variant

MultiBreak-SV – Detect Structural Variants from Single Molecule Sequencing data

MultiBreak-SV

: DESCRIPTION

MultiBreak-SV is a software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 MultiBreak-SV

:: MORE INFORMATION

Citation:

Characterization of Structural Variants with Single Molecule and Hybrid Sequencing Approaches.
Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.
Bioinformatics. 2014 Oct 28. pii: btu714.

GASV / GASVPro 20131001- Geometric Analysis of Structural Variants

GASV / GASVPro 20131001

:: DESCRIPTION

GASV / GASVPro (Geometric Analysis of Structural Variants) is a software for analysis of structural variation from paired-end sequencing and/or array-CGH data. This software has been tested used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GASV

:: MORE INFORMATION

Citation

S. Sindi, E. Helman, A. Bashir, B.J. Raphael. (2009)
A Geometric Approach for Classification and Comparison of Structural Variants.
Bioinformatics. 25: i222-i230.

SVGen v1 – Simulation of Structural Variants in Next-generation Sequencing data

SVGen v1

:: DESCRIPTION

SVGen is a tool with an extensive range of options to simulate germline and somatic SVs of various types and from short and long read sequencing platforms. The output from SVGen include BED files with SV regions, FASTA files with the simulated genome sequence and FASTQ files for short or long reads.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SVGen

:: MORE INFORMATION

Citation

LA Lima, H Yang, C Dong, K Wang.
SVGen: Simulation of structural variants in next-generation sequencing data.
(submitted)

SV-M 0.1 – Structural Variant Machine

SV-M 0.1

:: DESCRIPTION

SV-M is a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate.

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 SV-M

:: MORE INFORMATION

Citation

Dominik Grimm, Jörg Hagmann, Daniel Koenig, Detlef Weigel and Karsten Borgwardt:
Accurate indel prediction using paired-end short reads,
BMC Genomics 2013, 14:132 (27 February 2013)

SVEngine – Allele Specific and Haplotype Aware Structural Variants Simulator

SVEngine

:: DESCRIPTION

SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

SVEngine

:: MORE INFORMATION

Citation

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP

targetSeqView – Visualize Next Generation Sequencing Reads over Putative Structural Variants

targetSeqView

:: DESCRIPTION

targetSeqView is a probability-based score and visualization method to aid in distinguishing true structural variants from alignment artifacts.

::DEVELOPER

targetSeqView team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

  targetSeqView

:: MORE INFORMATION

Citation

Visualization and probability-based scoring of structural variants within repetitive sequences.
Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA.
Bioinformatics. 2014 Jun 1;30(11):1514-21. doi: 10.1093/bioinformatics/btu054.

SV-plaudit – Structural Variant Image Curation and Analysis

SV-plaudit

:: DESCRIPTION

SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis. SV-plaudit supports image generation sequencing data from BAM or CRAM files from Illumina paired-end sequencing, PacBio or Oxford Nanopore Technologies long-read sequencing, or 10X Genomics linked-read sequencing.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SV-plaudit

:: MORE INFORMATION

Citation:

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy064.
SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.
Belyeu JR et al.

MetaSV 0.5.4 – Structural-Variant caller for Next Generation Sequencing

MetaSV 0.5.4

:: DESCRIPTION

MetaSVM is an accurate method-aware merging algorithm for structural variations

::DEVELOPER

Roche Sequencing Solutions

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 MetaSV

:: MORE INFORMATION

Citation

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing.
Mohiyuddin M, Mu JC, Li J, Asadi NB, Gerstein MB, Abyzov A, Wong WH, Lam HY.
Bioinformatics. 2015 Apr 10. pii: btv204.

SQUID v1.5 – Structural Variant Detection from RNA-seq

SQUID v1.5

:: DESCRIPTION

SQUID is designed to detect both fusion-gene and non-fusino-gene transcriptomic structural variations from RNA-seq alignment.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

SQUID

:: MORE INFORMATION

Citation

Genome Biol. 2018 Apr 12;19(1):52. doi: 10.1186/s13059-018-1421-5.
SQUID: transcriptomic structural variation detection from RNA-seq.
Ma C, Shao M, Kingsford C.

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