Tag: Structural Variant

Socrates 0.95 – SOft Clip re-alignment To IdEntify Structural Variants

Socrates 0.95

:: DESCRIPTION

Socrates is a highly efficient and effective method for detecting genomic rearrangements in tumours that utilises split-read data. Socrates features single nucleotide resolution, high sensitivity, and high specificity in simulated data.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Socrates

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 22. [Epub ahead of print]
Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.
Schröder J1, Hsu A, Boyle SE, Macintyre G, Cmero M, Tothill RW, Johnstone RW, Shackleton M, Papenfuss AT.

Viola 1.0.0.dev10 – Structural Variant Signature Extractor

Viola 1.0.0.dev10

:: DESCRIPTION

Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures.

::DEVELOPER

Viola team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

Viola

:: MORE INFORMATION

Citation

Sugita I, Matsuyama S, Dobashi H, Komura D, Ishikawa S.
Viola: a structural variant signature extractor with user-defined classifications.
Bioinformatics. 2021 Sep 17:btab662. doi: 10.1093/bioinformatics/btab662. Epub ahead of print. PMID: 34534268.

BreakPoint Surveyor v1.1 – Pipeline for Structural Variant Visualization

BreakPoint Surveyor v1.1

:: DESCRIPTION

BreakPointSurveyor (BPS) is a set of core libraries (BreakPointSurveyor-Core) and workflows (this project) which, with optional external tools, evaluate genomic sequence data to discover, analyze, and provide a visual summary of breakpoint events.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BreakPointSurveyor

:: MORE INFORMATION

Citation

Wyczalkowski MA, Wylie KM, Cao S, McLellan MD, Flynn J, Huang M, Ye K, Fan X, Chen K, Wendl MC, Ding L.
BreakPoint Surveyor: a pipeline for structural variant visualization.
Bioinformatics. 2017 Oct 1;33(19):3121-3122. doi: 10.1093/bioinformatics/btx362. PMID: 28582538; PMCID: PMC5870665.

RAPTR-SV 0.0.15 – Hybrid Method for Detection of Structural Variants

RAPTR-SV 0.0.15

:: DESCRIPTION

RAPTR-SV (ReAdPair spliT – Read Structural Variant) uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data

::DEVELOPER

RAPTR-SV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOSX
  • JDK for Java
  • MrsFAST

:: DOWNLOAD

 RAPTR-SV

:: MORE INFORMATION

Citation

RAPTR-SV: a hybrid method for the detection of structural variants.
Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, Reecy JM, Schroeder S, Van Tassell CP, Sonstegard TS, Liu GE.
Bioinformatics. 2015 Feb 16. pii: btv086.

Manta 1.6.0 – Structural Variant and Indel Caller for Mapped Sequencing data

Manta 1.6.0

:: DESCRIPTION

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Manta

:: MORE INFORMATION

Citation

Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications.
Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, K?llberg M, Cox AJ, Kruglyak S, Saunders CT.
Bioinformatics. 2015 Dec 8. pii: btv710

Lumpy 0.3.1 – Structural Variant Discovery

Lumpy 0.3.1

:: 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

:: 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]

SAMBLASTER 0.1.26 – Duplicate Marking and Structural Variant Read Extraction

SAMBLASTER 0.1.26

:: DESCRIPTION

samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.

::DEVELOPER

Greg Faust (gf4ea@virginia.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAMBLASTER 

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 7. [Epub ahead of print]
SAMBLASTER: fast duplicate marking and structural variant read extraction.
Faust GG1, Hall IM.

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 Kronenberg, Shapiro 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.

DELLY 0.8.7 – integrated Split-read and Paired-end based Structural Variant Discovery in Deep sequencing data

DELLY 0.8.7

:: 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

svviz 1.5.2 – A Read Viewer for Validating Structural Variants

svviz 1.5.2

:: 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