tanghaibao / allhicView external linksLinks
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
☆60Jan 3, 2025Updated last year
Alternatives and similar repositories for allhic
Users that are interested in allhic are comparing it to the libraries listed below
Sorting:
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆177Oct 20, 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
- scripts to parse and analyse MCScanX collinearity output☆32Mar 3, 2020Updated 5 years ago
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆254Jan 5, 2026Updated last month
- ☆78Jun 12, 2020Updated 5 years ago
- Guided synteny alignment between duplicated genomes (within specified quota constraint)☆59Sep 5, 2017Updated 8 years ago
- Fast and frugal disk based k-mer counter☆14Apr 1, 2021Updated 4 years ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆173May 30, 2021Updated 4 years ago
- Python programs for processing GFF3 files☆102Dec 15, 2025Updated 2 months ago
- TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes☆104Nov 17, 2025Updated 3 months ago
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆889Dec 22, 2025Updated last month
- Mapping pipeline for data generated using Arima-HiC☆81May 22, 2024Updated last year
- ☆29Jul 16, 2022Updated 3 years ago
- Generate an interactive dot plot from mummer or minimap alignments☆211Jan 17, 2024Updated 2 years ago
- k-mer based assembly evaluation☆338Jun 28, 2024Updated last year
- ☆16Aug 14, 2024Updated last year
- Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of …☆13May 29, 2020Updated 5 years ago
- ☆12Nov 23, 2020Updated 5 years ago
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated 10 months ago
- A reference-assisted assembly tool for producing draft chromosome sequences.☆42Jun 24, 2024Updated last year
- Fast alignment and preprocessing of chromatin profiles☆213Jan 17, 2026Updated 3 weeks ago
- The tools are used for displaying hic signal of genome☆24Jan 4, 2021Updated 5 years ago
- ☆24Apr 22, 2025Updated 9 months ago
- Same species annotation lift over pipeline.☆97Jul 21, 2023Updated 2 years ago
- Identification of conserved non-coding sequences in plants☆32Feb 4, 2026Updated last week
- The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".☆29Mar 19, 2021Updated 4 years ago
- The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)☆80Oct 12, 2018Updated 7 years ago
- ☆78Dec 4, 2019Updated 6 years ago
- T2Tools is a toolset contains several tools for T2T assembly, and it is under development.☆15Sep 17, 2025Updated 5 months ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆291Feb 10, 2026Updated last week
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆215Jun 25, 2025Updated 7 months ago
- Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche…☆86Jan 6, 2026Updated last month
- A KMER-based genome-wIde Assocation testing approach on polyploids☆41Feb 6, 2026Updated last week
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆159Nov 4, 2025Updated 3 months ago
- Synteny and Rearrangement Identifier☆447Apr 29, 2025Updated 9 months ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆554Feb 14, 2024Updated 2 years ago
- De novo annotation of young retrotransposons☆47Apr 12, 2022Updated 3 years ago
- software tools for haplotype assembly from sequence data☆228Feb 9, 2025Updated last year