Scripting analyses of genomes in Ensembl Plants
☆45Apr 22, 2026Updated 6 months ago
Alternatives and similar repositories for plant-scripts
Users that are interested in plant-scripts are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.☆23Aug 12, 2026Updated 2 months ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated last year
- Explore potential Biosynthetic Gene Clusters in plant genomes. This tool is originally sourced from antiSMASH 4.0.☆40Feb 26, 2026Updated 8 months ago
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- scripts for the project of seven thaliana genomes assembly☆42May 22, 2021Updated 5 years ago
- A web-based, interactive pangenome visualization tool☆21Apr 10, 2023Updated 3 years ago
- ☆27Jun 27, 2026Updated 4 months ago
- Tool for fully-automated inference of species trees from raw genome assemblies☆50Aug 25, 2026Updated 2 months ago
- ☆12Updated this week
- SINE annotation tool for plant genomes☆19Jan 21, 2024Updated 2 years ago
- Ancestry_HMM-S is program designed to infer adaptive introgression from population genomic data☆20Sep 25, 2023Updated 3 years ago
- Resistify is a program which rapidly identifies and classifies plant NLR and PRR genes from protein sequences. It is designed to be light…☆52Jul 22, 2026Updated 3 months ago
- Reference-agnostic Representation and Visualization of Pan-genomes☆19Sep 16, 2021Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Long read aligner for cyclic and acyclic pangenome graphs☆41Dec 20, 2023Updated 2 years ago
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆41Oct 17, 2026Updated last week
- The IntroBlocker ancestry inference algorithm☆18Oct 24, 2023Updated 3 years ago
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated last year
- Rust implementation of Flavia95's GFAtoVCF☆16Jan 17, 2022Updated 4 years ago
- Method for inferring path posterior probabilities and abundances from pangenome graph read alignments☆63Sep 6, 2025Updated last year
- A KMER-based genome-wIde Assocation testing approach on polyploids☆72Jul 29, 2026Updated 3 months ago
- ☆21Dec 13, 2024Updated last year
- Deep Learning Framework for Transposable Element Discovery and Annotation☆12Aug 18, 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.
- a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).☆20Dec 5, 2023Updated 2 years ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆38Apr 28, 2026Updated 6 months ago
- Pan-genome Construction and Population Structure Variation Calling pipeline☆46Sep 13, 2024Updated 2 years ago
- GFA visualization tool - Rust reimplementation of odgi viz☆15May 2, 2026Updated 5 months ago
- Study of TE evolution in a population of genomes☆12Dec 11, 2023Updated 2 years ago
- A Nextflow workflow to generate lift over files for any pair of genomes☆76Aug 26, 2026Updated 2 months ago
- ☆23Oct 30, 2022Updated 4 years ago
- EasyHap is a cross-platform toolkit for regional haplotype analysis and visualization using phased VCF data from fungal, plant, and anima…☆21Oct 10, 2026Updated 2 weeks ago
- Long-read aligner to pangenome graphs☆29May 20, 2024Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- High-precision TE Annotator☆168Dec 4, 2025Updated 10 months ago
- Hybrid error correction approach for long reads using overlap graph☆11Sep 26, 2023Updated 3 years ago
- SRF: Satellite Repeat Finder☆110Jan 8, 2024Updated 2 years ago
- This is a method to find telomeres and centromeres in plants.☆43Jun 17, 2023Updated 3 years ago
- convert variation graph alignments to coverage maps over nodes☆28Jan 21, 2026Updated 9 months ago
- This is the standalone version of the EviAnn pipeline☆187Oct 7, 2026Updated 3 weeks ago
- Constructing a pangenome gene graph☆212Aug 11, 2025Updated last year