Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
☆20Jul 10, 2024Updated last year
Alternatives and similar repositories for sim3C
Users that are interested in sim3C are comparing it to the libraries listed below
Sorting:
- FreeHi-C pipeline for high fidelity Hi-C data simulation.☆12Jul 13, 2021Updated 4 years ago
- Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.☆24Jun 26, 2025Updated 8 months ago
- Unzip assembly graphs with Hi-C data and/or long reads.☆27Sep 20, 2024Updated last year
- ☆16Dec 25, 2024Updated last year
- Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.☆25Feb 11, 2026Updated 2 weeks ago
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated 9 months ago
- A haplotype-resolved and telomere-to-telomere genome assembly pipeline (PHap) tailored for autopolyploids, relying solely on common seque…☆19Jul 29, 2025Updated 7 months ago
- ☆10Jan 27, 2025Updated last year
- MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data☆11Mar 8, 2025Updated 11 months ago
- A library to analyse the structure of 1d loops and simulate loop extrusion by loop extruding factors.☆11Feb 10, 2025Updated last year
- Genome annotation pre-publication results☆25Updated this week
- Web based viewer for small to medium GFA format files, similar to Bandage☆12Nov 14, 2025Updated 3 months ago
- Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning☆28Aug 14, 2024Updated last year
- GWAS software that can handle autopolyploids☆32Oct 14, 2025Updated 4 months ago
- General purpose utility related to GAF files☆29Jan 27, 2026Updated last month
- ☆29Jul 16, 2022Updated 3 years ago
- Some components that speed up and reduce resource cost for original ALLHiC☆14Jun 21, 2025Updated 8 months ago
- Red-C data processing☆15Apr 18, 2023Updated 2 years ago
- HiFi error modeler and simulator with ploidy☆11Feb 12, 2026Updated 2 weeks ago
- Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling …☆13Dec 22, 2025Updated 2 months ago
- An effective alignment tool for long noisy 3C data (e.g. Pore-C and C-walk)☆14Oct 23, 2024Updated last year
- The software involved in the MetaPhase project, as described in G3 (http://dx.doi.org/10.1534/g3.114.011825)☆17Oct 12, 2018Updated 7 years ago
- ☆31Apr 7, 2025Updated 10 months ago
- Methylation analysis pipeline for genome graph☆15May 25, 2025Updated 9 months ago
- HiSV: a computational pipeline for structural variation detection from Hi-C data☆18Jun 20, 2025Updated 8 months ago
- Copy Number Variations (CNV) Simulator☆11Jul 30, 2018Updated 7 years ago
- T2Tools is a toolset contains several tools for T2T assembly, and it is under development.☆15Sep 17, 2025Updated 5 months ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆35Apr 23, 2025Updated 10 months ago
- Software for estimating genome-wide genealogies for thousands of samples☆40Oct 17, 2025Updated 4 months ago
- building a human pangenome from the HPRCy1v2 genbank accessioned assemblies☆15Feb 13, 2023Updated 3 years ago
- ☆16Mar 16, 2017Updated 8 years ago
- ☆16Mar 17, 2023Updated 2 years ago
- ☆32Jan 3, 2025Updated last year
- Blazing fast toolkit to work with .hic and .cool files☆42Feb 23, 2026Updated last week
- conserved non-coding sequence☆16Feb 21, 2022Updated 4 years ago
- Haplotype phaser for next-generation sequencing data☆13Jan 13, 2022Updated 4 years ago
- The IntroBlocker ancestry inference algorithm☆17Oct 24, 2023Updated 2 years ago
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆14Nov 20, 2023Updated 2 years ago
- CATG (Collinearity-based Assembly correcTor GUI) is a tool that can correct genome assembly with collinearity and generate tour files for…☆17Jan 24, 2026Updated last month