GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
☆274Sep 26, 2026Updated this week
Alternatives and similar repositories for GraffiTE
Users that are interested in GraffiTE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- High-precision TE Annotator☆165Dec 4, 2025Updated 9 months ago
- Tandem repeat expansion detection or genotyping from long-read alignments☆173Mar 25, 2026Updated 6 months ago
- HELIANO is a software for detection and classification of Helitron-like elements.☆34Jul 13, 2026Updated 2 months ago
- MCHelper: An automatic tool to curate transposable element libraries☆50Updated this week
- Synteny and Rearrangement Identifier☆491Jul 1, 2026Updated 2 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Pangenome-based genome inference☆181Sep 15, 2026Updated last week
- Earl Grey: A fully automated TE curation and annotation pipeline☆226Sep 15, 2026Updated last week
- Application of pan-genome for population☆122Oct 26, 2025Updated 11 months ago
- TEtrimmer: a novel tool to automate manual curation of transposable elements☆117Jul 27, 2026Updated 2 months ago
- Jasmine: SV Merging Across Samples☆261Dec 20, 2024Updated last year
- Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation☆202Aug 17, 2026Updated last month
- Evaluating genome assemblies☆127Mar 3, 2026Updated 6 months ago
- A program for assessing the T2T genome continuity and completeness☆97Sep 8, 2026Updated 2 weeks ago
- Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome☆100Jan 28, 2026Updated 7 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.
- Evaluation and polishing workflows for T2T genome assemblies☆170Sep 15, 2026Updated last week
- A genomic k-mer counter (and sequence utility) with nice features.☆191Jul 21, 2026Updated 2 months ago
- Identification of transposable element families from pangenome polymorphisms☆57Aug 11, 2026Updated last month
- Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics☆128Apr 17, 2026Updated 5 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆250Sep 6, 2024Updated 2 years ago
- A genome completeness evaluation tool based on miniprot☆267Aug 17, 2026Updated last month
- Tool to plot synteny and structural rearrangements between genomes☆356Jul 27, 2026Updated 2 months ago
- An accurate GFF3/GTF lift over pipeline☆558Aug 1, 2023Updated 3 years ago
- Mumemto: multi-MUM and MEM finding across pangenomes☆137Updated this week
- 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.
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆40Oct 29, 2025Updated 10 months ago
- the pangenome graph builder☆518Jul 24, 2026Updated 2 months ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆38Apr 28, 2026Updated 4 months ago
- Haplotype-specific somatic copy number aberrations/profiling from long reads sequencing data☆89Sep 9, 2026Updated 2 weeks ago
- Constructing a pangenome gene graph☆212Aug 11, 2025Updated last year
- Kmer Analysis of Pileups for Genotyping☆41Jul 16, 2026Updated 2 months ago
- Panacus is a tool for computing statistics for GFA-formatted pangenome graphs☆139Sep 8, 2026Updated 2 weeks ago
- Annotation helper tool for the manual curation of transposable element consensus sequences☆56Aug 26, 2026Updated last month
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆419Aug 25, 2026Updated last month
- 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 list of software for pangenomics☆200Sep 16, 2026Updated last week
- Structural Variant Identification Method using Genome Assemblies☆147Sep 16, 2022Updated 4 years ago
- This is the standalone version of the EviAnn pipeline☆186Sep 10, 2026Updated 2 weeks ago
- Phased structural variant discovery in pangenomes☆43Sep 18, 2026Updated last week
- haplotypic duplication identification tool☆295Oct 30, 2025Updated 10 months ago
- MEGAnE☆34Sep 13, 2023Updated 3 years ago
- Construct and Analyze the North American Vitis pangenome☆29Aug 19, 2025Updated last year