Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
☆105Sep 1, 2022Updated 3 years ago
Alternatives and similar repositories for Clair
Users that are interested in Clair are comparing it to the libraries listed below
Sorting:
- Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing☆173Dec 26, 2023Updated 2 years ago
- Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling☆341Feb 26, 2026Updated last week
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- ☆84Mar 3, 2025Updated last year
- Structural variation caller using third generation sequencing☆637Dec 18, 2025Updated 2 months ago
- Tools for the analysis of structural variation in genomes☆81Feb 23, 2026Updated 2 weeks ago
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆106Jun 6, 2021Updated 4 years ago
- Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs☆26Apr 29, 2024Updated last year
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 11 months ago
- A method for variant graph genotyping based on exact alignment of k-mers☆87Apr 1, 2019Updated 6 years ago
- ☆10Dec 28, 2023Updated 2 years ago
- ☆286Dec 29, 2025Updated 2 months ago
- PEPPER-Margin-DeepVariant☆257Jan 12, 2024Updated 2 years ago
- ☆46Jun 21, 2020Updated 5 years ago
- ☆35Feb 20, 2020Updated 6 years ago
- A Strategy for Building and Using a Human Reference Pangenome☆70May 29, 2020Updated 5 years ago
- Long read aligner☆114May 26, 2023Updated 2 years ago
- Long read based human genomic structural variation detection with cuteSV☆277Sep 30, 2025Updated 5 months ago
- BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer☆17Jun 15, 2023Updated 2 years ago
- nPoRe: n-Polymer Realigner for improved pileup-based variant calling☆18Jul 11, 2022Updated 3 years ago
- NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…☆308Mar 18, 2024Updated last year
- Read-based phasing of genomic variants, also called haplotype assembly☆409Dec 31, 2025Updated 2 months ago
- Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…☆12Jan 22, 2020Updated 6 years ago
- A tool set to assess the quality of the per read phasing and reduce the errors.☆13Jun 25, 2020Updated 5 years ago
- Long read / genome alignment software☆310Dec 16, 2025Updated 2 months ago
- Ploidy agnostic phasing pipeline and algorithm☆49Jan 3, 2024Updated 2 years ago
- Phase reads, assemble haplotypes and detect SVs☆19Nov 11, 2020Updated 5 years ago
- Code for phasing SVs with SNPs☆54Mar 27, 2020Updated 5 years ago
- ☆51Jun 25, 2024Updated last year
- Detect novel (and reference) STR expansions from short-read data☆70Dec 6, 2025Updated 3 months ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation