use variant nesting information to flter overlapping sites from vg deconstruct output
☆31Jun 12, 2025Updated 8 months ago
Alternatives and similar repositories for vcfbub
Users that are interested in vcfbub are comparing it to the libraries listed below
Sorting:
- Integrate multiple genome assemblies into a pangenome graph☆35Jun 9, 2022Updated 3 years ago
- GFA insert into GenomicSQLite☆49Jun 7, 2021Updated 4 years ago
- ☆18May 10, 2023Updated 2 years ago
- ☆29Aug 7, 2025Updated 6 months ago
- ☆15Jun 29, 2021Updated 4 years ago
- Constructing a pangenome gene graph☆204Aug 11, 2025Updated 6 months ago
- MEMO: MEM-based pangenome indexing for k-mer queries☆20Jun 11, 2024Updated last year
- Method for inferring path posterior probabilities and abundances from pangenome graph read alignments☆59Sep 6, 2025Updated 5 months ago
- convert variation graph alignments to coverage maps over nodes☆27Jan 21, 2026Updated last month
- A module for improving the insertion sequences of structural variant calls☆33Jul 14, 2021Updated 4 years ago
- Phased structural variant discovery in pangenomes☆39Dec 9, 2025Updated 2 months ago
- Pangenome-based genome inference☆156Dec 1, 2025Updated 3 months ago
- ☆101Apr 22, 2024Updated last year
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆234Feb 10, 2026Updated 3 weeks ago
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.☆37May 29, 2025Updated 9 months ago
- Genome Assembly Validation via Inter-SUNK distances in ONT reads☆15Feb 20, 2023Updated 3 years ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆36May 14, 2025Updated 9 months ago
- ☆23Sep 9, 2025Updated 5 months ago
- Set of script for the paper on the cattle graph genome☆13Jan 10, 2023Updated 3 years ago
- Panacus is a tool for computing statistics for GFA-formatted pangenome graphs☆119Feb 3, 2026Updated last month
- Construct and Analyze the North American Vitis pangenome☆29Aug 19, 2025Updated 6 months ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆210Jan 30, 2026Updated last month
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆34Oct 29, 2025Updated 4 months ago
- building a human pangenome from the HPRCy1v2 genbank accessioned assemblies☆15Feb 13, 2023Updated 3 years ago
- ☆44May 8, 2024Updated last year
- base-level dotplots from PAF alignments☆32Sep 18, 2025Updated 5 months ago
- Easy genomic regions for short-read variant calling☆45Sep 10, 2025Updated 5 months ago
- Kmer Analysis of Pileups for Genotyping☆36Jan 30, 2026Updated last month
- recompute GFA link overlaps☆25Sep 14, 2022Updated 3 years ago
- Structural Variant Identification Method using Genome Assemblies☆136Sep 16, 2022Updated 3 years ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- pangenome analyses for complete genomes of great apes (and gibbon)☆20Oct 12, 2024Updated last year
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆106Jun 6, 2021Updated 4 years ago
- your friendly pangenome graph genotyper☆10Feb 6, 2023Updated 3 years ago
- the pangenome graph evaluator☆29Apr 12, 2021Updated 4 years ago
- Bash scripts and data used in pantranscriptomic paper☆24Oct 21, 2022Updated 3 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 3 years ago
- BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer☆17Jun 15, 2023Updated 2 years ago
- ☆17Jan 5, 2021Updated 5 years ago