Deep learning framework for SV calling and genotyping
☆113Nov 8, 2023Updated 2 years ago
Alternatives and similar repositories for cue
Users that are interested in cue are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Detecting genome structural variants with deep learning in single molecule sequencing☆116Apr 9, 2025Updated last year
- Fast and accurate coordinate conversion between assemblies☆119Jun 1, 2026Updated last week
- Application of pan-genome for population☆121Oct 26, 2025Updated 7 months ago
- Structural variant toolkit for VCFs☆414May 22, 2026Updated 2 weeks ago
- Jasmine: SV Merging Across Samples☆254Dec 20, 2024Updated last year
- 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.
- Wally: Visualization of aligned sequencing reads and contigs☆125Oct 9, 2025Updated 8 months ago
- Updated figures for "A benchmarking of WGS-based structural variant callers" paper☆27Apr 3, 2022Updated 4 years ago
- Toolkit for calling structural variants using short or long reads☆115May 18, 2026Updated 3 weeks ago
- ☆35Aug 18, 2024Updated last year
- Toolset for SV simulation, comparison and filtering☆420Dec 1, 2023Updated 2 years ago
- Pangenome-based genome inference☆170Jun 2, 2026Updated last week
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated 2 years ago
- Structural Variant Identification Method using Genome Assemblies☆143Sep 16, 2022Updated 3 years ago
- ☆51Sep 4, 2025Updated 9 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A tutorial on structural variant calling for short read sequencing data☆43Oct 24, 2024Updated last year
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Apr 20, 2026Updated last month
- ☆19Nov 22, 2022Updated 3 years ago
- Transformer-based sequence correction method for genome assembly polishing☆104Mar 11, 2025Updated last year
- Population-scale genotyping using pangenome graphs☆199Jan 9, 2025Updated last year
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆55Mar 7, 2025Updated last year
- pbsv - PacBio structural variant (SV) calling and analysis tools☆166Feb 26, 2025Updated last year
- A Nextflow workflow to generate lift over files for any pair of genomes☆74Nov 19, 2025Updated 6 months ago
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Aug 24, 2022Updated 3 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A structural variation pipeline for short-read sequencing☆203Updated this week
- base-level dotplots from PAF alignments☆34Sep 18, 2025Updated 8 months ago
- Find and visualize rearrangements in DNA sequences☆55Updated this week
- Detect novel (and reference) STR expansions from short-read data☆71Dec 6, 2025Updated 6 months ago
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 6 months ago
- ☆101Apr 22, 2024Updated 2 years ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆109Jun 6, 2021Updated 5 years ago
- Graph realignment tools for structural variants☆168Dec 8, 2022Updated 3 years ago
- A method for variant graph genotyping based on exact alignment of k-mers☆87Apr 1, 2019Updated 7 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- TQSLE v1.0 released☆10Aug 29, 2023Updated 2 years ago
- Toolkit for VNTR genotyping and repeat-pan genome graph construction☆34Aug 18, 2025Updated 9 months ago
- SV calling for diploid assemblies☆31Mar 22, 2024Updated 2 years ago
- ☆18Jan 29, 2025Updated last year
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated last year
- Transfer HiFi read mappings from their own assembly contigs to a standard reference☆39Dec 30, 2025Updated 5 months ago
- An ultra-fast and efficient genomic tool for coverage calculation☆172Feb 9, 2026Updated 4 months ago