HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
☆254Jan 5, 2026Updated 2 months ago
Alternatives and similar repositories for HapHiC
Users that are interested in HapHiC are comparing it to the libraries listed below
Sorting:
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆167Oct 29, 2025Updated 4 months ago
- Yet another Hi-C scaffolding tool☆172Nov 4, 2024Updated last year
- C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C，Omni-C).☆90Jan 25, 2026Updated last month
- A novel genome assembly pipeline based on deep learning☆69Dec 2, 2024Updated last year
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated 11 months ago
- This is the standalone version of the EviAnn pipeline☆139Feb 5, 2026Updated 3 weeks ago
- Repeat-aware polishing genomes assembled using HiFi long reads☆98Nov 12, 2025Updated 3 months ago
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆178Oct 20, 2024Updated last year
- A program for assessing the T2T genome continuity☆92Dec 14, 2025Updated 2 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆233Sep 6, 2024Updated last year
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆69May 22, 2021Updated 4 years ago
- use long sequenced reads to close gaps in assemblies☆41Sep 4, 2018Updated 7 years ago
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆159Nov 4, 2025Updated 4 months ago
- Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning☆28Aug 14, 2024Updated last year
- Identify and find telomeres, or telomeric repeats in a genome.☆158Nov 24, 2025Updated 3 months ago
- Dynamic Elongation of a Genome Assembly Path☆25Feb 25, 2026Updated last week
- A genome completeness evaluation tool based on miniprot☆235Sep 18, 2025Updated 5 months ago
- ☆31Apr 7, 2025Updated 10 months ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆743Mar 18, 2025Updated 11 months ago
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆383Feb 24, 2026Updated last week
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆292Feb 25, 2026Updated last week
- ☆33Mar 19, 2025Updated 11 months ago
- Synteny and Rearrangement Identifier☆448Apr 29, 2025Updated 10 months ago
- ☆21Dec 8, 2025Updated 2 months ago
- De novo chromosome-level scaffolding and phasing tool using Hi-C☆30Nov 23, 2025Updated 3 months ago
- haplotypic duplication identification tool☆275Oct 30, 2025Updated 4 months ago
- ☆29Feb 5, 2026Updated last month
- High-precision TE Annotator☆151Dec 4, 2025Updated 3 months ago
- A organelle de novo genome assembly toolkit☆74Feb 22, 2025Updated last year
- Any Way to Show Multi genomic Synteny☆218Jul 4, 2025Updated 8 months ago
- source code for EVM☆122Nov 29, 2024Updated last year
- An ultra-fast and efficient genomic tool for coverage calculation☆170Feb 9, 2026Updated 3 weeks ago
- Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).☆104Jul 23, 2024Updated last year
- Neural network classification of TE☆97Oct 9, 2025Updated 4 months ago
- Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation☆181Dec 16, 2025Updated 2 months ago
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆449Oct 20, 2025Updated 4 months ago
- k-mer based assembly evaluation☆339Jun 28, 2024Updated last year
- ☆41Jun 8, 2023Updated 2 years ago