ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
☆179Oct 20, 2024Updated last year
Alternatives and similar repositories for ALLHiC
Users that are interested in ALLHiC are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Genome scaffolding based on HiC data in heterozygous and high ploidy genomes☆60Jan 3, 2025Updated last year
- 3D de novo assembly (3D DNA) pipeline☆225Nov 29, 2023Updated 2 years ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆214Mar 9, 2026Updated last month
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆267Jan 5, 2026Updated 4 months ago
- Fast and accurately polish the genome generated by long reads.☆243Jan 9, 2025Updated last year
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆69May 22, 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
- k-mer based assembly evaluation☆343Jun 28, 2024Updated last year
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated last year
- haplotypic duplication identification tool☆284Oct 30, 2025Updated 6 months ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆903Updated this week
- Extensive de-novo TE Annotator☆443Apr 5, 2026Updated last month
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated last year
- Synteny and Rearrangement Identifier☆463Mar 17, 2026Updated last month
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Fast and accurate de novo assembler for long reads☆400May 10, 2024Updated last year
- 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…☆26Mar 11, 2023Updated 3 years ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆294Feb 25, 2026Updated 2 months ago
- Yet another Hi-C scaffolding tool☆180Nov 4, 2024Updated last year
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆434Mar 28, 2024Updated 2 years ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆564Feb 14, 2024Updated 2 years ago
- ☆29Jul 16, 2022Updated 3 years ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆237Sep 6, 2024Updated last year
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆768Apr 15, 2026Updated 2 weeks ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Mapping pipeline for data generated using Arima-HiC☆84May 22, 2024Updated last year
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆457Apr 12, 2026Updated 3 weeks ago
- Generate an interactive dot plot from mummer or minimap alignments☆215Jan 17, 2024Updated 2 years 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
- A One-Click System for Analyzing Loop-Resolution Hi-C Experiments☆480Aug 31, 2025Updated 8 months ago
- use long sequenced reads to close gaps in assemblies☆40Sep 4, 2018Updated 7 years ago
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- Fast genome analysis from unassembled short reads☆320Apr 8, 2024Updated 2 years ago
- source code for EVM☆124Nov 29, 2024Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆170Oct 29, 2025Updated 6 months ago
- A parallel wrapper for LTR_FINDER☆55Mar 8, 2026Updated last month
- ☆78Jun 12, 2020Updated 5 years ago
- Repeat-aware polishing genomes assembled using HiFi long reads☆101Apr 7, 2026Updated 3 weeks ago
- Convert Tandem Repeat Finder dat file output into gff3 format☆31Nov 9, 2025Updated 5 months ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆210Nov 18, 2022Updated 3 years ago