2832 days ago
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
HiC-Pro was designed to process Hi-C data,...zed contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C pr...nzyme such as DNase Hi-C. In practice, HiC-Pro can be used to process di...ta. http://nservant.github.io/HiC-Pro/2305 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yi...2283 days ago
HiGlass: a tool for exploring genomic contact matrices and tracks.
...that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is...2118 days ago
sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
Required python modules biopython intervaltree numpy scipy tqdm PyYAML1963 days ago
3D de novo assembly (3D DNA) pipeline
...Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly. For the original version of the pipeline and to reproduce the Hs2-HiC and the AaegL4 genomes report...1517 days ago
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs an...1115 days ago
632 days ago