ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
☆180Oct 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☆229Nov 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…☆220Jun 30, 2026Updated 2 months ago
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆286Aug 10, 2026Updated last month
- Fast and accurately polish the genome generated by long reads.☆247Jan 9, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆70May 22, 2021Updated 5 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☆355Jul 6, 2026Updated 2 months ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated 2 years ago
- haplotypic duplication identification tool☆295Oct 30, 2025Updated 10 months ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆931Updated this week
- Extensive de-novo TE Annotator☆469Sep 10, 2026Updated 2 weeks ago
- Synteny and Rearrangement Identifier☆491Jul 1, 2026Updated 2 months ago
- Fast and accurate de novo assembler for long reads☆407May 10, 2024Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆76Jun 4, 2026Updated 3 months 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…☆26Mar 11, 2023Updated 3 years ago
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆302Updated this week
- Yet another Hi-C scaffolding tool☆183Nov 4, 2024Updated last year
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆444Mar 28, 2024Updated 2 years ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆576Feb 14, 2024Updated 2 years ago
- ☆29Jul 16, 2022Updated 4 years ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆250Sep 6, 2024Updated 2 years ago
- Mapping pipeline for data generated using Arima-HiC☆85May 22, 2024Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆814May 31, 2026Updated 3 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…☆467Jun 17, 2026Updated 3 months ago
- Generate an interactive dot plot from mummer or minimap alignments☆220Jan 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☆490Sep 15, 2026Updated last week
- use long sequenced reads to close gaps in assemblies☆40Sep 4, 2018Updated 8 years ago
- source code for EVM☆128Updated this week
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- Fast genome analysis from unassembled short reads☆328Apr 8, 2024Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C☆26Jan 14, 2021Updated 5 years ago
- A parallel wrapper for LTR_FINDER☆57Mar 8, 2026Updated 6 months ago
- ☆78Jun 12, 2020Updated 6 years ago
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆184Jun 23, 2026Updated 3 months ago
- Repeat-aware polishing genomes assembled using HiFi long reads☆105Apr 7, 2026Updated 5 months ago
- A organelle de novo genome assembly toolkit☆82Feb 22, 2025Updated last year
- Convert Tandem Repeat Finder dat file output into gff3 format☆32Sep 7, 2026Updated 2 weeks ago