Alignment-free genotyper for SNPs and short indels, implemented in Python.
☆58Mar 7, 2025Updated last year
Alternatives and similar repositories for kage
Users that are interested in kage are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆102Apr 22, 2024Updated 2 years ago
- Fast and accurate coordinate conversion between assemblies☆119Jun 1, 2026Updated 3 months ago
- ☆50Jul 2, 2026Updated 2 months ago
- recompute GFA link overlaps☆26Sep 14, 2022Updated 3 years ago
- ☆46Apr 18, 2026Updated 4 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Long-read aligner to pangenome graphs☆29May 20, 2024Updated 2 years ago
- COsine SImilarity-based Genotyper using pangenomes☆36Updated this week
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆27Apr 29, 2024Updated 2 years ago
- your friendly pangenome graph genotyper☆10Feb 6, 2023Updated 3 years ago
- Targeted genotyper for complex polymorphic genes☆47Updated this week
- alignment to variation graph inducer☆165Jul 29, 2026Updated last month
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆250Updated this week
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆38Apr 28, 2026Updated 4 months ago
- Differential quantification of alternative splicing events on spliced pangenome graphs☆16Jan 30, 2026Updated 7 months ago
- 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.
- Constructing a pangenome gene graph☆212Aug 11, 2025Updated last year
- A Generative Pre-Trained Transformer Package for Pangenomes☆53May 19, 2025Updated last year
- ☆11Dec 9, 2022Updated 3 years ago
- plane sweep filtering genome alignments☆24Jul 25, 2026Updated last month
- General purpose utility related to GAF files☆37Aug 6, 2026Updated last month
- genotyping by Mapping-free ALternate-allele detection of known VAriants☆10Mar 6, 2023Updated 3 years ago
- Long read aligner for cyclic and acyclic pangenome graphs☆41Dec 20, 2023Updated 2 years ago
- Pangenome-based genome inference☆180Aug 18, 2026Updated 2 weeks ago
- Reference bias measuring toolkit☆22Mar 12, 2026Updated 5 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.
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 9 months ago
- An accurate aligner of long reads to a variation graph, based on co-linear chaining☆35May 23, 2025Updated last year
- GFA insert into GenomicSQLite☆49Jun 7, 2021Updated 5 years ago
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 10 months ago
- A method for variant graph genotyping based on exact alignment of k-mers☆88Apr 1, 2019Updated 7 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 3 years ago
- Rust implementation of Flavia95's GFAtoVCF☆16Jan 17, 2022Updated 4 years ago
- Code for building and testing variant ranking strategies☆18Apr 13, 2026Updated 4 months ago
- CPANG19 - Computational PANGenomics (2019)☆12May 7, 2020Updated 6 years 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 versatile pairwise aligner for genomic and spliced nucleotide sequences☆24Sep 12, 2025Updated 11 months ago
- Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer☆13Dec 18, 2023Updated 2 years ago
- Graph realignment tools for structural variants☆171Dec 8, 2022Updated 3 years ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆36Aug 18, 2025Updated last year
- Genotyping of copy number sensitive allele-specific haplotypes☆29Aug 28, 2026Updated last week
- Differential k-mer analysis☆42Jan 29, 2024Updated 2 years ago
- SRF: Satellite Repeat Finder☆108Jan 8, 2024Updated 2 years ago