SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, …
Hi-C (genomic analysis technique) - Wikipedia
The general procedure of Hi-C involves first crosslinking chromatin material using formaldehyde. [ 3 ][ 4 ] Then, the chromatin is solubilized and fragmented, and interacting loci are re-ligated together to create a genomic library of chimeric DNA molecules. [ 4 ]
c-zhou/yahs: Yet another Hi-C scaffolding tool - GitHub
YaHS is a scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies.
Methods - DNA Zoo
Check out this tutorial and barrel clover assembly video to get an idea of how JBAT works. Follow this link to download the .hic and .assembly files and follow along with the tutorial yourself!
Recently, Shilpa Garg and colleagues developed “diploid assembly” (DipAsm), which combines Arima High Coverage Hi-C long-range conformation data with high-fidelity (HiFi) long reads to assemble individual chromosomes in one day (Figure 2)15. These latest developments in phased genome assembly solve one of the biggest
Visualization and analysis software for Hi-C data - GitHub
Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly. Juicebox was created by Jim Robinson, Neva C. Durand, and Erez Lieberman Aiden.
EndHiC: assemble large contigs into chromosome-level scaffolds …
Dec 8, 2022 · These results suggest that EndHiC is able to assemble the large contigs generated from the current HiFi reads into chromosome-level scaffolds, with high accuracy in the cluster, order and orientation, for a certain part of diploid plant and animal genomes.
Efficient iterative Hi-C scaffolder based on N-best neighbors
Nov 27, 2021 · While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic species, the inexpensive Hi-C sequencing technology, capable of capturing the chromosomal profile of a genome, is now widely used to complete the task.
YaHS: yet another Hi-C scaffolding tool - Oxford Academic
Dec 16, 2022 · In comparisons with SALSA2 and pin_hic, two recently published Hi-C scaffolding tools, applied to both simulated and real data, YaHS generated genome assemblies of higher accuracy and contiguity, and was more robust to assembly errors.
Arima-HiC: A simple and robust Hi-C workflow - Arima Genomics
Jan 30, 2024 · How Hi-C technology can be used to uncover genome organization structures for epigenetic studies as well as scaffold contigs into chromosome-spanning genome assemblies. An overview of the Arima-HiC workflow, from Arima-HiC sample preparation to library preparation and Illumina sequencing.