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.

Lumpy 0.3.0 – Structural Variant Discovery

Lumpy 0.3.0

:: DESCRIPTION

Lumpy is a new probabilistic framework that we have developed to integrate multiple structural variation signals such as discordant paired-end alignments and split-read alignments. While it is clear that integrating all SV signals is important for sensitive discovery, most existing (including our own Hydra) tools only exploit one signal. Lumpy integrates multiple signals in order to improve sensitivity and breakpoint resolution. This is especially important for cancer genome analysis where tumor heterogeneity causes potentially important rearrangements occur with less supporting alignments in the sampled DNA.

::DEVELOPER

The Quinlan Lab ,Ira Hall Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C ++ Compiler
  • the GNU Scientific Library (GSL).

:: DOWNLOAD

  Lumpy

:: MORE INFORMATION

Citation

Layer RM, Quinlan AR, Hall IM,
LUMPY: A probabilistic framework for structural variant discovery.
arXiv:1210.2342v2 [q-bio.GN]

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

svviz 1.4.0 – A Read Viewer for Validating Structural Variants

svviz 1.4.0

:: DESCRIPTION

svviz visualizes high-throughput sequencing data relevant to a structural variant.

::DEVELOPER

Noah Spies

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 svviz

:: MORE INFORMATION

Citation

svviz: a read viewer for validating structural variants.
Spies N, Zook JM, Salit M, Sidow A.
Bioinformatics. 2015 Aug 18. pii: btv478

DELLY 0.7.3 – integrated Split-read and Paired-end based Structural Variant Discovery in Deep sequencing data

DELLY 0.7.3

:: DESCRIPTION

DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

::DEVELOPER

Korbel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DELLY

:: MORE INFORMATION

Citation

DELLY: structural variant discovery by integrated paired-end and split-read analysis
Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M. Stütz; Vladimir Benes; Jan O. Korbel
Bioinformatics 2012 28: i333-i339

Wham 1.8.0 – Identifying Structural Variants of Biological Consequence

Wham 1.8.0

:: DESCRIPTION

Wham (Whole-genome Alignment Metrics) is a structural variant (SV) caller that integrates several sources of mapping information to identify SVs.

::DEVELOPER

Zev KronenbergShapiro Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Wham

:: MORE INFORMATION

Citation:

Wham: Identifying Structural Variants of Biological Consequence.
Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M.
PLoS Comput Biol. 2015 Dec 1;11(12):e1004572. doi: 10.1371/journal.pcbi.1004572.