Explores Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively. It integrates many technologies developed for the Integrative Genomics Viewer with a broad ensemble of methods specifically designed for handling 2D contact data. Individual maps can be normalized (corrected for experimental bias), compared to one-dimensional tracks (such as gene tracks or chromatin immunoprecipitation sequencing data), and compared to 2D feature lists (such as loop and domain annotations).
Applies virtual rearrangements, or ‘structural variations’, to an initial set of DNA fragments. instaGRAAL constructs one-dimensional (1D) genome structures that are consistent with the 3D contact data. It designs a genomic bin randomly without replacement, then picks a number of partner bins with probabilities that depend on the measured contact frequencies. This tool can find and position duplicated regions.
Combines Hi-C linkage information with the ambiguous-edge information from a genome assembly graph to better resolve uniting orientations. SALSA is an application that exploits the information of genomic proximity in Hi-C data sets for long range scaffolding of de novo genome assemblies. This method can produce centromere to telomere scaffolds of chromosomes and telomere to telomere scaffolds.
Extracts metagenome-assembled genomes (MAGs) from metagenomic shotgun sequencing experiments. bin3C consists of an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs from a single time-point. It utilizes the unsupervised community detection algorithm Infomap to perform. The software can retrieve MAGs from metagenomes by combining conventional metagenome shotgun and Hi-C sequencing data. Furthermore, it was tested with short-read sequencing data.
Consists of a workflow including 15 bioinformatics tools. ARTwork can perform reads quality control, variant calling, reads trimming, de novo assembly, reference-based scaffolding, assembly quality control, genome typing and annotation, and ultimately tracking all metadata created during the data processing lifecycle. It contains also a document-oriented database to store information about each whole genome sequencing (WGS) data received.
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