ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
☆178Oct 20, 2024Updated last year
Alternatives and similar repositories for ALLHiC
Users that are interested in ALLHiC are comparing it to the libraries listed below
Sorting:
- 3D de novo assembly (3D DNA) pipeline☆222Nov 29, 2023Updated 2 years ago
- Genome scaffolding based on HiC data in heterozygous and high ploidy genomes☆60Jan 3, 2025Updated last year
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆215Updated this week
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆254Jan 5, 2026Updated 2 months ago
- Fast and accurately polish the genome generated by long reads.☆240Jan 9, 2025Updated last year
- k-mer based assembly evaluation☆339Jun 28, 2024Updated last year
- Extensive de-novo TE Annotator☆430Updated this week
- haplotypic duplication identification tool☆275Oct 30, 2025Updated 4 months ago
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆69May 22, 2021Updated 4 years ago
- Yet another Hi-C scaffolding tool☆172Nov 4, 2024Updated last year
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆188May 17, 2024Updated last year
- The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)☆80Oct 12, 2018Updated 7 years ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆292Feb 25, 2026Updated last week
- Python library to facilitate genome assembly, annotation, and comparative genomics☆890Updated this week
- Fast and accurate de novo assembler for long reads☆398May 10, 2024Updated last year
- Tools for fast and flexible genome assembly scaffolding and improvement☆559Feb 14, 2024Updated 2 years ago
- Synteny and Rearrangement Identifier☆448Apr 29, 2025Updated 10 months ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆431Mar 28, 2024Updated last year
- A gap-closing software tool that uses long reads to enhance genome assembly.☆233Sep 6, 2024Updated last year
- Mapping pipeline for data generated using Arima-HiC☆82May 22, 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
- 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
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to a…☆25Mar 11, 2023Updated 2 years ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆743Mar 18, 2025Updated 11 months ago
- source code for EVM☆122Nov 29, 2024Updated last year
- Generate an interactive dot plot from mummer or minimap alignments☆212Jan 17, 2024Updated 2 years ago
- Fast genome analysis from unassembled short reads☆313Apr 8, 2024Updated last year
- Repeat-aware polishing genomes assembled using HiFi long reads☆98Nov 12, 2025Updated 3 months ago
- GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis…☆54Feb 27, 2020Updated 6 years ago
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- Fast alignment and preprocessing of chromatin profiles☆214Jan 17, 2026Updated last month
- ☆78Jun 12, 2020Updated 5 years ago
- ☆29Jul 16, 2022Updated 3 years ago
- Convert Tandem Repeat Finder dat file output into gff3 format☆30Nov 9, 2025Updated 3 months ago
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆475Aug 31, 2025Updated 6 months ago
- A parallel wrapper for LTR_FINDER☆55Mar 23, 2025Updated 11 months ago
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆167Oct 29, 2025Updated 4 months ago
- De-Novo Repeat Discovery Tool☆231Jul 21, 2025Updated 7 months ago