SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (a...Tags: SMASH, alignment-free, tool, find, visualise, rearrangements, pairs, DNA, sequences
2319 days ago
Tags: AccessSyRI, finding, genomic, rearrangements, sequence, differences, whole-genome, assemblies
1547 days ago
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. CSAR-web can serve as a convenient and useful scaffolding tool ...Tags: CSAR-web, web, server, contig, scaffolding, algebraic, rearrangements
1478 days ago
Tags: Syri, compares, alignments, chromosome-level, assemblies, synteny, structural, rearrangements
696 days ago
ReConPlot: an R package for the visualization and interpretation of genomic rearrangements
ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-qua...Tags: ReConPlot, R, package, visualization, interpretation, genomic, rearrangements
135 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the ne...Tags: PaReBrick, Parallel, Rearrangements, Breaks, identification, toolkit
932 days ago