stepwise 0.3 – Stepwise Detection of Recombination Breakpoints

stepwise 0.3

:: DESCRIPTION

A stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints.

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

:: DOWNLOAD

 stepwise

:: MORE INFORMATION

Citation

Graham, McNeney and Seillier-Moiseiwitsch.
Stepwise detection of recombination breakpoints in sequence alignments.
Bioinformatics. 2005 Mar 1;21(5):589-95. Epub 2004 Sep 23.

MATCHCLIPS 2 – Identifying the Breakpoints and CNVs

MATCHCLIPS 2

:: DESCRIPTION

MATCHCLIP is a program for identifying the breakpoints and CNVs based on the next generation sequence data using CIGAR strings.

::DEVELOPER

Hongzhe Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MATCHCLIP

:: MORE INFORMATION

Citation

Front Genet. 2013 Aug 16;4:157. doi: 10.3389/fgene.2013.00157. eCollection 2013.
MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads.
Wu Y1, Tian L, Pirastu M, Stambolian D, Li H.

SVseq 2.2 – Detecting exact Breakpoints of Deletions with Low-coverage Sequence data

SVseq 2.2

:: DESCRIPTION

SVseq2 is an improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SVseq2

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S6. doi: 10.1186/1471-2105-13-S6-S6.
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
Zhang J1, Wang J, Wu Y.

Destruct v0.4.19 – Accurate Rearrangement Detection using Breakpoint Specific Realignment

Destruct v0.4.19

:: DESCRIPTION

Destruct is a tool for joint prediction of rearrangement breakpoints from single or multiple tumour samples.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

Destruct 

:: MORE INFORMATION

YAHA 0.1.83 – Long-read Alignment with Optimal Breakpoint Detection

YAHA 0.1.83

:: DESCRIPTION

YAHA is a flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. It can output all the alignments found for each query, only the set of alignments that optimally cover each query, or add alignments that are similar to those that optimally cover the query.

::DEVELOPER

 Greg Faust (gf4ea@virginia.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 YAHA

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Oct 1;28(19):2417-24. Epub 2012 Jul 24.
YAHA: fast and flexible long-read alignment with optimal breakpoint detection.
Faust GG1, Hall IM.

TakeABreak 1.1.2 – Detect Inversion Breakpoints directly from raw NGS reads

TakeABreak 1.1.2

:: DESCRIPTION

TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime.

::DEVELOPER

colib’read project team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

 TakeABreak

:: MORE INFORMATION

Citation

Claire Lemaitre, Liviu Ciortuz and Pierre Peterlongo,
Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads
Proceedings of AlCoB 2014, in Algorithms for Computational Biology, LNCS vol. 8542, pp. 119–130.

MitoBreak – Mitochondrial DNA Breakpoints Database

MitoBreak

:: DESCRIPTION

MitoBreak provides a complete, quality checked and regularly updated list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially-duplicated (duplications) and linear mtDNAs.

::DEVELOPER

Filipe Pereira

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jan 1;42(1):D1261-8. doi: 10.1093/nar/gkt982.
MitoBreak: the mitochondrial DNA breakpoints database.
Damas J, Carneiro J, Amorim A, Pereira F.

NBC 1.0 – Neighborhood Breakpoint Conservation

NBC 1.0

:: DESCRIPTION

NBC (Neighborhood Breakpoint Conservation) is a method that identifies recurrent copy number variants in multiple individuals using Array Comparative Genomic Hybridization (aCGH).aCGH computes the ratio of test:reference DNA for probes located on the reference genome. NBC first uses a Bayesian changepoint algorithm to identify probes, called breakpoints, that change from low-to-high or high-to-low copy number with high probability. A binomial statistic is then applied to identify breakpoints and pairs of breakpoints that appear in a statistically significant number of individuals.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Java

:: DOWNLOAD

 NBC

:: MORE INFORMATION

Citation

A. Ritz, P.L. Paris, M.M. Ittmann, C. Collins, and B.J. Raphael. (2011)
Detection of Recurrent Rearrangement Breakpoints from Copy Number Data.
BMC Bioinformatics 2011, 12:114 doi:10.1186/1471-2105-12-114

Cassis 1.0 – Detect Genomic Rearrangement Breakpoints

Cassis 1.0

:: DESCRIPTION

Cassis is a software for precise detection of rearrangement breakpoints in whole (sequenced and assembled) genomes.

::DEVELOPER

Cassis team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Cassis

:: MORE INFORMATION

Citation

Baudet, C., Lemaitre, C., Dias, Z., Tannier, E., Tannier, E., Gautier, C., and Sagot, M.-F. (2010).
Cassis : precise detection of genomic rearrangement breakpoints.
Bioinformatics, 26(15), 1897-1898.

Breakpoint Calculator 0.2.1 – Calculate Breakpoint Counts for each pair and triplet of Genomes

Breakpoint Calculator 0.2.1

:: DESCRIPTION

Breakpoint Calculator calculates pairwise and three-way hidden breakpoint counts for each pair and triplet of genomes.The breakpoint calculator constructs a weighted graph from the adjacencies of the genomes in the alignment and computes a maximum weight perfect matching.

::DEVELOPER

Birte Kehr., Knut Reinert, and Aaron Darling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

  Breakpoint Calculator

:: MORE INFORMATION

Citation

Birte Kehr, Knut Reinert, Aaron Darling
Hidden breakpoints in genome alignments
WABI 2012