SVDetect 0.8b – Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data

SVDetect 0.8b

:: DESCRIPTION

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SVDetect

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1895-6.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

SvABA 1.1.0 – Structural Variation and Indel Detection by local Assembly

SvABA 1.1.0

:: DESCRIPTION

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.

::DEVELOPER

Jeremiah Wala (jwala@broadinstitute.org) — Rameen Berkoukhim lab — Dana Farber Cancer Institute, Boston, MA.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SvABA

:: MORE INFORMATION

Citation

Wala JA, Bandopadhayay P, Greenwald NF, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.
SvABA: genome-wide detection of structural variants and indels by local assembly.
Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13. PMID: 29535149; PMCID: PMC5880247.

Meerkat 0.189 – Identify Structural Variations

Meerkat 0.189

:: DESCRIPTION

Meerkat is designed to identify structure variations (SVs) from paired end high throughput sequencing data. It predicts SVs from discordant read pairs (pairs that mapped to reference genome in unexpected way).

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Meerkat

:: MORE INFORMATION

Citation

Cell. 2013 May 9;153(4):919-29. doi: 10.1016/j.cell.2013.04.010.
Diverse mechanisms of somatic structural variations in human cancer genomes.
Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ.

TIGRA-SV v0.1.3.3 – Conduct Targeted local Assembly of Structural Variation

TIGRA-SV v0.1.3.3

:: DESCRIPTION

TIGRA-SV is a program that conducts targeted local assembly of structural variants (SV) using the iterative graph routing assembly (TIGRA) algorithm (L. Chen, unpublished). It takes as input a list of putative SV calls and a set of bam files that contain reads mapped to a reference genome such as NCBI build36. For each SV call, it assembles the set of reads that were mapped or partially mapped to the region of interest (ROI) in the corresponding bam files. Instead of outputing a single consensus sequence, TIGRA-SV outputs all the alternative alleles in the ROI as long as they received sufficient sequence coverage (usually >= 2x). It is shown that TIGRA-SV is quite effective at improving the SV prediction accuracy in short reads analysis and can produce accurate breakpoint sequences that are valuable to understand the origin, mechanism and pathology underlying the SVs.

::DEVELOPER

The Genome Institute at Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 TIGRA-SV

:: MORE INFORMATION

BACH / BACH-MIX – Bayesian 3D constructor for Hi-C data / Characterize Structural Variations of Chromatin Folding

BACH / BACH-MIX

:: DESCRIPTION

BACH is a novel Bayesian probabilistic approach for analyzing Hi-C data. BACH takes the Hi-C contact matrix and local genomic features (restriction enzyme cutting frequencies, GC content and sequence uniqueness) as input and produces, via MCMC computation, the posterior distribution of three-dimensional (3D) chromosomal structure

BACH-MIX is an extended BACH algorithm to characterize structural variations of chromatin folding

::DEVELOPER

Jun Liu

:: SCREENSHOTS

bach

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 BACH , BACH-MIX

:: MORE INFORMATION

Citation

Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. (2013)
Bayesian Inference of Spatial Organizations of Chromosomes.
PLoS Computational Biology 9(1): e1002893.

Genome STRiP 2.00.1529 – Discovering and Genotyping Structural Variations using Sequencing data

Genome STRiP 2.00.1529

:: DESCRIPTION

Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals, but can also process single genomes.

::DEVELOPER

Genome STRiP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • R package

:: DOWNLOAD

  Genome STRiP

:: MORE INFORMATION

Citation

Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA
Large multiallelic copy number variations in humans
Nature Genetics (2015) doi:10.1038/ng.3200

Handsaker RE, Korn JM, Nemesh J, McCarroll SA
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Nature genetics 43, 269-276 (2011)

BreakDancer 1.4.5 – Structural Variation Caller for Paired-end Data

BreakDancer 1.4.5

:: DESCRIPTION

BreakDancer is a  package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Perl/C++

:: DOWNLOAD

 BreakDancer

:: MORE INFORMATION

Citation:

Ken Chen, John W Wallis, Michael D McLellan, David E Larson, Joelle M Kalicki, Craig S Pohl, Sean D McGrath, Michael C Wendl, Qunyuan Zhang2, Devin P Locke, Xiaoqi Shi, Robert S Fulton, Timothy J Ley, Richard K Wilson, Li Ding1 & Elaine R Mardis1
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
Nature Methods 6, 677 – 681 (2009)

VariationHunter 0.04 – Structural Variation Detection

VariationHunter 0.04

:: DESCRIPTION

VariationHunter-CL (VariationHunter-CommonLaw)is a package of programs need to find structural variations which mappings of paired-end reads are known.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C Complier

:: DOWNLOAD

 VariationHunter

:: MORE INFORMATION

Citation

Next Generation VariationHunter: Combinatorial Algorithms for Transposon Insertion Discovery
Fereydoun Hormozdiari, Iman Hajirasouliha, Phuong Dao, Faraz Hach, Deniz Yorukoglu, Can Alkan, Evan E. Eichler, S. Cenk Sahinalp
Bioinformatics 2010 Jun 15;26(12):i350-i357

laSV 1.0.2 – Local Assembly based Structural Variation Discovery tool

laSV 1.0.2

:: DESCRIPTION

laSV is a software that employs a local de novo assembly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets.

::DEVELOPER

ZLab, University of Massachusetts Medical School, Worcester, MA, USA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 laSV

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Sep 30;43(17):8146-56. doi: 10.1093/nar/gkv831. Epub 2015 Aug 17.
Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.
Zhuang J, Weng Z

Hydra 0.5.3 / Hydra-Multi – Structural Variation Discovery with Paired-end-mapping

Hydra 0.5.3 / Hydra-Multi

:: DESCRIPTION

Hydra detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose “signatures” corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments.

Hydra-Multi is a paired-end read structural variant discovery tool that is capable of integrating signals from hundreds of samples.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Hydra / Hydra-Multi

:: MORE INFORMATION

Citation:

Population-based structural variation discovery with Hydra-Multi.
Lindberg MR, Hall IM, Quinlan AR.
Bioinformatics. 2014 Dec 2. pii: btu771.

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
Aaron R. Quinlan1, Royden A. Clark1, Svetlana Sokolova1, Mitchell L. Leibowitz1, Yujun Zhang2, Matthew E. Hurles2, Joshua C. Mell3 and Ira M. Hall
Genome Res. 2010. 20: 623-635