A haplotype-resolved and telomere-to-telomere genome assembly pipeline (PHap) tailored for autopolyploids, relying solely on common sequencing data including long-reads and Hi-C.
☆17Jul 29, 2025Updated 7 months ago
Alternatives and similar repositories for PHap
Users that are interested in PHap are comparing it to the libraries listed below
Sorting:
- An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes☆45Sep 22, 2025Updated 5 months ago
- A tool for quick and accurate calculation of syntenic diversity.☆42Sep 22, 2025Updated 5 months ago
- gghic makes visualization of Hi-C/-like data easily in R☆24Jan 23, 2026Updated last month
- ☆24Apr 22, 2025Updated 10 months ago
- ☆28Oct 20, 2023Updated 2 years ago
- base-level dotplots from PAF alignments☆32Sep 18, 2025Updated 5 months ago
- Everything but the kitchen sink☆12Feb 6, 2025Updated last year
- Genome annotation pre-publication results☆25Updated this week
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 4 months ago
- Extracting paths from assembly graphs☆24Apr 26, 2024Updated last year
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆16Jan 12, 2026Updated last month
- ☆12Jun 7, 2024Updated last year
- General purpose utility related to GAF files☆29Jan 27, 2026Updated last month
- General purpose tools for every-day sequencing bioinformatics. If you use any of these tools, please acknowledge this repository (there a…☆12Oct 13, 2020Updated 5 years ago
- Colour and fill scales for 'ggplot2' using colour spaces.☆15Feb 24, 2021Updated 5 years ago
- Unzip assembly graphs with Hi-C data and/or long reads.☆27Sep 20, 2024Updated last year
- ☆31Apr 7, 2025Updated 10 months ago
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆23Apr 25, 2024Updated last year
- ☆32Jan 3, 2025Updated last year
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- ☆38Dec 29, 2025Updated 2 months ago
- Centromere mapping and annotation pipeline☆22Feb 13, 2026Updated 2 weeks ago
- A plant organellar Graphical Fragment Assembly toolkit☆16Sep 10, 2025Updated 5 months ago
- ☆19Feb 15, 2025Updated last year
- conserved non-coding sequence☆16Feb 21, 2022Updated 4 years ago
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆14Nov 20, 2023Updated 2 years ago
- CAncer Standards Long-read Evaluation☆52Nov 7, 2025Updated 3 months ago
- Genotyping of copy number sensitive allele-specific haplotypes☆27Nov 6, 2025Updated 3 months ago
- ☆16Dec 25, 2024Updated last year
- Data Simulation for Life Science and Breeding☆42Jun 13, 2025Updated 8 months ago
- ☆24Dec 3, 2025Updated 2 months ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆44Oct 13, 2024Updated last year
- Robust Eukaryotic Annotation Toolkit☆18Feb 28, 2025Updated last year
- This is a method to find telomeres and centromeres in plants.☆42Jun 17, 2023Updated 2 years ago
- Simple tools for working with Hi-C data☆18Dec 19, 2018Updated 7 years ago
- A rapid and accurate ensemble pipeline for graph-based variant genotyping with lower depth of short reads☆49Sep 22, 2025Updated 5 months ago
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆23Feb 16, 2026Updated last week
- Tandem Repeats Finder: a program to analyze DNA sequences☆20Jul 30, 2025Updated 6 months ago