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.
☆272Aug 11, 2026Updated last 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☆164Dec 4, 2025Updated 8 months ago
- Tandem repeat expansion detection or genotyping from long-read alignments☆170Mar 25, 2026Updated 4 months ago
- HELIANO is a software for detection and classification of Helitron-like elements.☆34Jul 13, 2026Updated last month
- MCHelper: An automatic tool to curate transposable element libraries☆50Aug 5, 2026Updated last week
- Synteny and Rearrangement Identifier☆485Jul 1, 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.
- Pangenome-based genome inference☆177Aug 6, 2026Updated last week
- Earl Grey: A fully automated TE curation and annotation pipeline☆221Aug 11, 2026Updated last week
- Application of pan-genome for population☆121Oct 26, 2025Updated 9 months ago
- TEtrimmer: a novel tool to automate manual curation of transposable elements☆118Jul 27, 2026Updated 3 weeks ago
- Jasmine: SV Merging Across Samples☆260Dec 20, 2024Updated last year
- Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation☆200Updated this week
- Evaluating genome assemblies☆126Mar 3, 2026Updated 5 months ago
- A program for assessing the T2T genome continuity and completeness☆95Feb 28, 2026Updated 5 months ago
- Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome☆100Jan 28, 2026Updated 6 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.
- A genomic k-mer counter (and sequence utility) with nice features.☆185Jul 21, 2026Updated 3 weeks ago
- Evaluation and polishing workflows for T2T genome assemblies☆164Jun 26, 2026Updated last month
- Identification of transposable element families from pangenome polymorphisms☆57Aug 11, 2026Updated last week
- Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics☆127Apr 17, 2026Updated 4 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆243Sep 6, 2024Updated last year
- A genome completeness evaluation tool based on miniprot☆260Updated this week
- Tool to plot synteny and structural rearrangements between genomes☆353Jul 27, 2026Updated 3 weeks ago
- An accurate GFF3/GTF lift over pipeline☆548Aug 1, 2023Updated 3 years ago
- Mumemto: multi-MUM and MEM finding across pangenomes☆134Jul 29, 2026Updated 2 weeks ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆40Oct 29, 2025Updated 9 months ago
- the pangenome graph builder☆510Jul 24, 2026Updated 3 weeks ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆38Apr 28, 2026Updated 3 months ago
- Haplotype-specific somatic copy number aberrations/profiling from long reads sequencing data☆86Updated this week
- Constructing a pangenome gene graph☆212Aug 11, 2025Updated last year
- Kmer Analysis of Pileups for Genotyping☆40Jul 16, 2026Updated last month
- Panacus is a tool for computing statistics for GFA-formatted pangenome graphs☆138Updated this week
- Annotation helper tool for the manual curation of transposable element consensus sequences☆55Mar 5, 2025Updated last year
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆409Aug 4, 2026Updated 2 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A list of software for pangenomics☆197Updated this week
- Structural Variant Identification Method using Genome Assemblies☆147Sep 16, 2022Updated 3 years ago
- This is the standalone version of the EviAnn pipeline☆183Aug 11, 2026Updated last week
- Phased structural variant discovery in pangenomes☆43Jul 27, 2026Updated 3 weeks ago
- haplotypic duplication identification tool☆295Oct 30, 2025Updated 9 months ago
- MEGAnE☆34Sep 13, 2023Updated 2 years ago
- Construct and Analyze the North American Vitis pangenome☆29Aug 19, 2025Updated 11 months ago