Deep learning framework for SV calling and genotyping
☆115Nov 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☆117Apr 9, 2025Updated last year
- Fast and accurate coordinate conversion between assemblies☆119Jun 1, 2026Updated 2 months ago
- Structural variant toolkit for VCFs☆422May 22, 2026Updated 3 months ago
- Application of pan-genome for population☆121Oct 26, 2025Updated 10 months ago
- Jasmine: SV Merging Across Samples☆259Dec 20, 2024Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Wally: Visualization of aligned sequencing reads and contigs☆127Jul 10, 2026Updated last month
- SV calling for diploid assemblies☆32Mar 22, 2024Updated 2 years ago
- Updated figures for "A benchmarking of WGS-based structural variant callers" paper☆27Apr 3, 2022Updated 4 years ago
- Pangenome-based genome inference☆179Aug 18, 2026Updated last week
- Toolkit for calling structural variants using short or long reads☆117Aug 21, 2026Updated last week
- ☆36Aug 18, 2024Updated 2 years ago
- Toolset for SV simulation, comparison and filtering☆425Dec 1, 2023Updated 2 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆27Apr 29, 2024Updated 2 years ago
- HAT is a set of tools for calling de novo variants from whole-genome sequencing data.☆24Nov 18, 2025Updated 9 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A tutorial on structural variant calling for short read sequencing data☆46Oct 24, 2024Updated last year
- Structural Variant Identification Method using Genome Assemblies☆147Sep 16, 2022Updated 3 years ago
- ☆52Sep 4, 2025Updated 11 months ago
- ☆19Nov 22, 2022Updated 3 years ago
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Apr 20, 2026Updated 4 months ago
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆58Mar 7, 2025Updated last year
- Transformer-based sequence correction method for genome assembly polishing☆109Mar 11, 2025Updated last year
- Population-scale genotyping using pangenome graphs☆201Jan 9, 2025Updated last year
- pbsv - PacBio structural variant (SV) calling and analysis tools☆168Jul 15, 2026Updated last month
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- A structural variation pipeline for short-read sequencing☆206Updated this week
- 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 4 years ago
- A Nextflow workflow to generate lift over files for any pair of genomes☆75Updated this week
- Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity☆18Mar 10, 2022Updated 4 years ago
- Detect novel (and reference) STR expansions from short-read data☆71Dec 6, 2025Updated 8 months ago
- Find and visualize rearrangements in DNA sequences☆56Jun 3, 2026Updated 2 months ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆119Jun 6, 2021Updated 5 years ago
- ☆102Apr 22, 2024Updated 2 years ago
- Graph realignment tools for structural variants☆171Dec 8, 2022Updated 3 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 method for variant graph genotyping based on exact alignment of k-mers☆88Apr 1, 2019Updated 7 years ago
- Tandem repeat genotyping from long reads☆27Updated this week
- TQSLE v1.0 released☆10Aug 29, 2023Updated 3 years ago
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated last year
- An ultra-fast and efficient genomic tool for coverage calculation☆175Jun 9, 2026Updated 2 months ago
- ☆18Jan 29, 2025Updated last year
- Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads☆87May 27, 2026Updated 3 months ago