Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
☆100Feb 27, 2023Updated 3 years ago
Alternatives and similar repositories for HipSTR
Users that are interested in HipSTR are comparing it to the libraries listed below
Sorting:
- A tool for profiling long STRs from short reads☆105Apr 19, 2021Updated 4 years ago
- lobSTR: a short tandem repeat profiler for next generation sequencing data☆54Oct 12, 2023Updated 2 years ago
- TREDPARSE: HLI Short Tandem Repeat (STR) caller☆25Aug 20, 2020Updated 5 years ago
- Method for detecting STR expansions from short-read sequencing data☆63Dec 15, 2021Updated 4 years ago
- Structural variant detection and association testing☆108Feb 2, 2023Updated 3 years ago
- PopSTR - A Population based microsatellite genotyper☆32Oct 23, 2023Updated 2 years ago
- Reference files for running HipSTR with various organisms☆17Feb 3, 2018Updated 8 years ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated 2 weeks ago
- Genotype and phase short tandem repeats using Illumina whole-genome sequencing data☆31May 10, 2021Updated 4 years ago
- A tool for estimating repeat sizes☆206Jan 30, 2024Updated 2 years ago
- Detect novel (and reference) STR expansions from short-read data☆70Dec 6, 2025Updated 3 months ago
- Graph realignment tools for structural variants☆165Dec 8, 2022Updated 3 years ago
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- Structural variation and indel detection by local assembly☆252Sep 16, 2025Updated 5 months ago
- Integrated Variant Caller☆17Mar 15, 2018Updated 7 years ago
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆143Aug 24, 2025Updated 6 months ago
- ☆26Aug 10, 2021Updated 4 years ago
- Detects human contamination in bam files☆16Sep 10, 2020Updated 5 years ago
- A method for variant graph genotyping based on exact alignment of k-mers☆87Apr 1, 2019Updated 6 years ago
- Naive PCA for genotype data☆10Jul 27, 2016Updated 9 years ago
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆279May 21, 2025Updated 9 months ago
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Sep 2, 2025Updated 6 months ago
- SRF: Satellite Repeat Finder☆103Jan 8, 2024Updated 2 years ago
- A suite of tools for detecting expansions of short tandem repeats☆85Jul 6, 2023Updated 2 years ago
- A read extraction and realignment tool for next generation sequencing data☆105Oct 29, 2022Updated 3 years ago
- Toolkit for calling structural variants using short or long reads☆115Feb 11, 2026Updated 3 weeks ago
- Population-scale genotyping using pangenome graphs☆196Jan 9, 2025Updated last year
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 3 years ago
- Pangenome graphs (review article on graph-based pangenomic methods)☆72Apr 15, 2020Updated 5 years ago
- Reducing reference bias using multiple population reference genomes☆34May 27, 2024Updated last year
- Stupid Simple (ba)Sh Testing - A functional software testing framwork☆23Nov 8, 2023Updated 2 years ago
- Exact Tandem Repeat Finder (not a TRF replacement)☆51Oct 22, 2019Updated 6 years ago
- Accurate microsatellite genotypes from high-throughput resequencing data☆24Sep 26, 2014Updated 11 years ago
- Jasmine: SV Merging Across Samples☆241Dec 20, 2024Updated last year
- Segmented HAPlotype Estimation and Imputation Tool☆98Aug 28, 2023Updated 2 years ago
- Tandem Repeats Finder: a program to analyze DNA sequences☆199Jan 16, 2023Updated 3 years ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆398Aug 30, 2025Updated 6 months ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 2 years ago
- Scalable gVCF merging and joint variant calling for population sequencing projects☆176Apr 12, 2024Updated last year