AgilePindelFilter 20130517 – Identification of Insertions and Deletions as well as large scale Rearrangements using Exome data

AgilePindelFilter 20130517

:: DESCRIPTION

AgilePindelFilter enables the rapid filtering, screening and sorting of indel variants derived from an exome sequencing experiment to allow the rapid detection of possible deleterious variants.

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

AgilePindelFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgilePindelFilter

:: MORE INFORMATION

Citation

Robust diagnostic genetic testing using solution capture enrichment and a novel variant-filtering interface.
Watson CM, Crinnion LA, Morgan JE, Harrison SM, Diggle CP, Adlard J, Lindsay HA, Camm N, Charlton R, Sheridan E, Bonthron DT, Taylor GR, Carr IM.
Hum Mutat. 2014 Apr;35(4):434-41. doi: 10.1002/humu.22490.

COSER – Compare Genomes with Segmental Duplications and Rearrangements

COSER

:: DESCRIPTION

COSER is a software to COmpare genomes with SEgmental duplications and Rearrangement

::DEVELOPER

Laboratory for Computational Biology and Bioinformatics (LCBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 COSER

:: MORE INFORMATION

Citation

Comparing genomes with rearrangements and segmental duplications.
Shao M, Moret BM.
Bioinformatics. 2015 Jun 15;31(12):i329-i338. doi: 10.1093/bioinformatics/btv229.

SMASH – Find and Visualise Genomic Rearrangements

SMASH

:: DESCRIPTION

Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMASH

:: MORE INFORMATION

Citation

Diogo Pratas, Raquel M. Silva, Armando J. Pinho, Paulo J. S. G. Ferreira.
An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.
Scientific Reports, 2015 (Accepted).

CAR – Contig Assembly of Prokaryotic Draft Genomes Using Rearrangements

CAR

:: DESCRIPTION

CAR is an efficient and more accurate tool for assembling contigs of a prokaryotic draft genome based on a reference genome.

::DEVELOPER

Algorithm and Bioinformatics Laboratory, Department of Computer Science, National Tsing Hua University, Taiwan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CAR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 28;15(1):381.
CAR: contig assembly of prokaryotic draft genomes using rearrangements.
Lu C, Chen KT, Huang SY, Chiu HT.

Bellerophon 1.03 – Detecting Large Scale Genome Rearrangements

Bellerophon 1.03

:: DESCRIPTION

Bellerophon is a hybrid split-read and paired-read method for detecting and classifying interchromosomal structural variants at base-pair level.

::DEVELOPER

Computational Biology lab @ Case (CBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • SamTools
  • Perl

:: DOWNLOAD

 Bellerophon

:: MORE INFORMATION

Citation

Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data.
Hayes M, Li J.
BMC Bioinformatics. 2013;14 Suppl 5:S6. doi: 10.1186/1471-2105-14-S5-S6.

GRIL 1.0.0 – Genome Inversion and Rearrangement Locator

GRIL 1.0.0

:: DESCRIPTION

GRIL is a tool that can be used to identify the location of rearrangements and inversions in the backbone of a set of DNA sequences. GRIL works by identifying exactly matching regions present in all sequences under consideration and organizing them into groups of collinear regions. GRIL removes small regions of collinearity that appear unlikely to be true sequence rearrangements based on user-specified criteria such as the length of the collinear region and the percent sequence identity of the collinear region. The size of sequences that GRIL can be applied to is dependent on the amount of available memory.

::DEVELOPER

Genome Evolution Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 GRIL

:: MORE INFORMATION

Citation:

Aaron E. Darling, Bob Mau, Frederick R. Blattner and Nicole T. Perna
GRIL: genome rearrangement and inversion locator
Bioinformatics (2004) 20 (1): 122-124.

BAIT 1.4 – Organizing Genomes and Mapping Rearrangements in Single Cells

BAIT 1.4

:: DESCRIPTION

BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

::DEVELOPER

Terry Fox Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • SAMtools
  • BEDtools
  • R
  • DNAcopy R package
  • gplots R package.

:: DOWNLOAD

 BAIT

:: MORE INFORMATION

Citation

Genome Med. 2013 Sep 13;5(9):82.
BAIT: Organizing genomes and mapping rearrangements in single cells.
Hills M1, O’Neill K, Falconer E, Brinkman R, Lansdorp PM.

UniMoG – Genome Rearrangement

UniMoG

:: DESCRIPTION

UniMoG (former DCJ) is a software tool unifying five genome rearrangement distance models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion only and translocation only. It allows computing all of these five distances between pairs of genomes represented as sequences of oriented common blocks.

DCJ (double-cut-and-join) computes the double-cut-and-join distance between two genomes and an optimal sorting scenario that transforms one genome into the other. It operates on the most general model of genomes with a mixed collection of linear and circular chromosomes. The sorting process includes all classical rearrangement operations such as inversions, translocations, transpositions, block interchanges, fusions and fissions.

::DEVELOPER

Rafael Friesen, Julia Mixtacki, Jens Stoye

:: SCREENSHOTS

UniMoG

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

DCJ

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 1;28(19):2509-11. Epub 2012 Jul 18.
UniMoG–a unifying framework for genomic distance calculation and sorting based on DCJ.
Hilker R1, Sickinger C, Pedersen CN, Stoye J.

A. Bergeron, J. Mixtacki, J. Stoye.
A unifying view of genome rearrangements
Proceedings of WABI 2006, LNBI 4175, 163-173, 2006.

Virtual hybridation 0.5.9 / pipviewer 0.3.9 – Exploring Genome Rearrangements

Virtual hybridation 0.5.9 / pipviewer 0.3.9

:: DESCRIPTION

Virtual hybridation computes comparative genomics datasets by computational mapping of probes on extant genomes.

Pipviewer is a visualizer for multiple alignements of genomic sequences. It highlights conserved regions and allows basic anotations. Its main goal is to find conserved probes for the construction of gene order data sets.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

pipviewer

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 Virtual hybridation / pipviewer

:: MORE INFORMATION

Citation

EXPLORING GENOME REARRANGEMENTS USING VIRTUAL HYBRIDIZATION
M. BELCAID,A. BERGERON,A. CHATEAU, C. CHAUVE, Y. GINGRAS,G. POISSON1 AND M. VENDETTE

DeCoLT – Lateral Gene Transfer, Rearrangement, Reconciliation

DeCoLT

:: DESCRIPTION

The software DeCoLT computes adjacencies (or any type of relation, like regulation, interaction, functional relationships) between ancestral genes from gene phylogenies reconciled with a species phylogeny according to duplications, losses and lateral gene transfer. It takes as input (1) a species tree (2) a set of extant genes (3) a set of exant adjacencies (relations) between extant genes and (4) reconciled gene trees which leaves are the extant genes.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

DeCoLT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 15:S4. doi: 10.1186/1471-2105-14-S15-S4. Epub 2013 Oct 15.
Lateral gene transfer, rearrangement, reconciliation.
Patterson M, Szöllősi G, Daubin V, Tannier E.