AggloIndel – Detect Structural Variations

AggloIndel

:: DESCRIPTION

AggloIndel which is a tool to detect structural variations, is specifically designed to cluster short-read paired-end data into possibly overlapping predictions for deletions and insertions. The method does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity, polyploidy, etc. Taking paired ends mapped to a reference genome as input, it iteratively merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into account.

::DEVELOPER

Roland Wittler , Bielefeld University

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux / Mac / Windows
Java

:: DOWNLOAD

AggloIndel

:: MORE INFORMATION

Citation

Roland Wittler
Unraveling overlapping deletions by agglomerative clustering.,
BMC Genomics. 2013;14 Suppl 1:S12. doi: 10.1186/1471-2164-14-S1-S12. Epub 2013 Jan 21.

Weaver – Allele-Specific Quantification of Structural Variations in Cancer Genomes

Weaver

:: DESCRIPTION

Weaver quantifies allele-specific copy number alteration and allele-specific structural variation in cancer genome using whole-genome sequencing reads.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Weaver

:: MORE INFORMATION

Citation

Allele-Specific Quantification of Structural Variations in Cancer Genomes.
Li Y, Zhou S, Schwartz DC, Ma J.
Cell Syst. 2016 Jul;3(1):21-34. doi: 10.1016/j.cels.2016.05.007.

SWAN 0.3.0 – Statistical Structural Variation ANalyzer

SWAN 0.3.0

:: DESCRIPTION

SWAN is the first to introduce a statistically verifiable heterogeneity SV model to the community. As in SWAN, the genetic material sampled is no longer viewed as a homogenous mutant or reference sample but explicitly modeled as a mixture of both mutant and reference sequences with their fractions estimable.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
R

:: DOWNLOAD

SWAN

:: MORE INFORMATION

Citation

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
LC Xia, S Sakshuwong, E Hopmans, J Bell, S Grimes, D Siegmund, H Ji, Nancy Zhang.
Nucleic Acids Research 44 (15), e126 (2016)

Tangram 0.3.1 – Structural Variation(SV) Detection based on MOSAIK Alignments

Tangram 0.3.1

:: DESCRIPTION

Tangram is a command line toolbox for structural variation(SV) detection based on MOSAIK alignments.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
C/C++ Compiler

:: DOWNLOAD

Tangram

:: MORE INFORMATION

Citation

Toolbox for mobile-element insertion detection on cancer genomes.
Lee WP, Wu J, Marth GT.
Cancer Inform. 2015 Feb 12;14(Suppl 1):37-44. doi: 10.4137/CIN.S24657.

Tangram: a comprehensive toolbox for mobile element insertion detection.
Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT.
BMC Genomics. 2014 Sep 16;15:795. doi: 10.1186/1471-2164-15-795.

Sniffles 1.0.11 – Structural Variation Caller using Third Generation Sequencing

Sniffles 1.0.11

:: DESCRIPTION

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.

::DEVELOPER

Sniffles team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Sniffles

:: MORE INFORMATION

Citation

Accurate detection of complex structural variations using single-molecule sequencing.
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC.
Nat Methods. 2018 Jun;15(6):461-468. doi: 10.1038/s41592-018-0001-7.

ClipCrop – Detecting Structural Variations using Soft-clipping Information

ClipCrop

:: DESCRIPTION

ClipCrop is a tool for detecting structural variations using soft-clipping information From SAM files.

::DEVELOPER

Nagasaki Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
SHRiMP2 or bwa

:: DOWNLOAD

ClipCrop

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S7. doi: 10.1186/1471-2105-12-S14-S7.
ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information.
Suzuki S, Yasuda T, Shiraishi Y, Miyano S, Nagasaki M.