PPL (Pore-C PipLine) is a set of tools to process, evaluate and visualize the multi-way contacts experiment based on 3C and ONT long reads sequencing.
☆16Apr 22, 2025Updated last year
Alternatives and similar repositories for PPL-Toolbox
Users that are interested in PPL-Toolbox are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A chromosome-level polyploid phasing scaffolding tool☆18Updated this week
- An effective alignment tool for long noisy 3C data (e.g. Pore-C and C-walk)☆16Oct 23, 2024Updated last year
- ☆52Nov 24, 2025Updated 7 months ago
- C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C, Omni-C).☆103Updated this week
- 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
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Python-based web scraper for extracting gene summaries from GeneCards.☆12Oct 3, 2024Updated last year
- Enumerating bubbles in pangenome graphs☆15Updated this week
- We developed a protocol of in situ high throughput multi-way contact long read Pore-C sequencing (in situ HiPore-C), a strategy that inte…☆23Mar 17, 2024Updated 2 years ago
- BAMixChecker: A fast and efficient tool for sample matching checkup☆16Jun 12, 2022Updated 4 years ago
- ☆20Jun 30, 2026Updated 2 weeks ago
- Tool for globally phasing diploid assembly graphs with orthogonal data☆43Nov 25, 2024Updated last year
- Discovery of communities in Pore-C concatemers☆16Feb 12, 2025Updated last year
- ☆13May 27, 2025Updated last year
- base-level dotplots from PAF alignments☆35Sep 18, 2025Updated 10 months ago
- 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.
- Variant Calling for the HPRC2☆16May 26, 2026Updated last month
- ☆33Apr 7, 2025Updated last year
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆46Oct 13, 2024Updated last year
- A Python implementation for BH-FDR and HiCCUPS☆54Dec 29, 2025Updated 6 months ago
- ☆29Jul 16, 2022Updated 4 years ago
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated last year
- SUPBUB is a tool that, in linear time, finds out superbubbles(special graph-structures) in a directed graph.☆12Sep 19, 2019Updated 6 years ago
- Very simple and configurable all-in-one dotplot program☆14Apr 1, 2023Updated 3 years ago
- Python library for simple and complex indels.☆12Jan 22, 2024Updated 2 years ago
- 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.
- Genome Assembly Validation via Inter-SUNK distances in ONT reads☆16Feb 20, 2023Updated 3 years ago
- GWAS software that can handle autopolyploids☆34Oct 14, 2025Updated 9 months ago
- Everything but the kitchen sink☆13Feb 6, 2025Updated last year
- Unzip assembly graphs with Hi-C data and/or long reads.☆29May 7, 2026Updated 2 months ago
- plane sweep filtering genome alignments☆24May 23, 2026Updated last month
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆24Feb 16, 2026Updated 5 months ago
- Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning☆29Aug 14, 2024Updated last year
- an interactive visualization and interpretation framework of reference-projected pangenome graphs☆42Feb 15, 2025Updated last year
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat☆29Apr 24, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆35Jun 24, 2026Updated 3 weeks ago
- Pan-3D genome analysis of soybean Hi-C data☆12Mar 6, 2023Updated 3 years ago
- Telomere-to-Telomere diploid Indian Genome☆15Mar 5, 2026Updated 4 months ago
- General purpose utility related to GAF files☆31May 20, 2026Updated 2 months ago
- CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…☆27Apr 16, 2025Updated last year
- A fast and efficient tool for converting chromatin interaction data between genome assemblies☆78Jul 22, 2025Updated 11 months ago
- An ultra-fast gzip file tools☆28Jun 23, 2026Updated 3 weeks ago