Genotyping lots of samples with big pangenomes
☆11Oct 30, 2025Updated 4 months ago
Alternatives and similar repositories for genotypify
Users that are interested in genotypify are comparing it to the libraries listed below
Sorting:
- lace up GFA files using panSN path name sub-ranges to coordinate the lacing☆14Jul 30, 2025Updated 7 months 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
- COsine SImilarity-based Genotyper using pangenomes☆31Feb 13, 2026Updated last month
- Everything but the kitchen sink☆13Feb 6, 2025Updated last year
- ☆15Jun 29, 2021Updated 4 years ago
- ☆18Jan 29, 2025Updated last year
- A toolkit for exploring regions of variation in pangenomes☆14Feb 14, 2026Updated last month
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 4 months ago
- your friendly pangenome graph genotyper☆10Feb 6, 2023Updated 3 years ago
- Rust implementation of Flavia95's GFAtoVCF☆16Jan 17, 2022Updated 4 years ago
- a precise pangenome browser combining linear and graph-based pan-genome☆13Jul 16, 2024Updated last year
- Rust package for constructing and analyzing phylogenies. (unpolished & unmaintained)☆15May 1, 2025Updated 10 months ago
- ☆19May 10, 2023Updated 2 years ago
- ☆10Jan 18, 2023Updated 3 years ago
- PanGenome Graph Building with the first 100 assemblies from the 1000G ONT Sequencing Consortium☆12Apr 5, 2025Updated 11 months ago
- implicit pangenome graph☆97Mar 13, 2026Updated last week
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 7 months ago
- ANI based satellite annotation☆25Mar 2, 2026Updated 2 weeks ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆36May 14, 2025Updated 10 months ago
- ☆21Dec 13, 2024Updated last year
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆23Feb 16, 2026Updated last month
- ☆101Apr 22, 2024Updated last year
- A viewer for multiple alignment format (MAF) files in JBrowse 2☆14Updated this week
- Statistics and analysis for variation graphs☆49Dec 17, 2024Updated last year
- Unzip assembly graphs with Hi-C data and/or long reads.☆27Sep 20, 2024Updated last year
- The GitHub for CLUES2, a method for inferring and evaluating evidence for selection.☆18Apr 9, 2025Updated 11 months ago
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆13Oct 1, 2025Updated 5 months ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 2025Updated 9 months ago
- A web-based, interactive pangenome visualization tool☆21Apr 10, 2023Updated 2 years ago
- alignment to variation graph inducer☆157Mar 6, 2026Updated last week
- Identification of transposable element families from pangenome polymorphisms☆56Jun 3, 2025Updated 9 months ago
- somatic SV calling on matched tumor-normal co-assembly graphs☆22Aug 1, 2024Updated last year
- ☆16Mar 17, 2023Updated 3 years ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆44Oct 13, 2024Updated last year
- Inferring natural selection by comparative population genomic analysis across species☆26Oct 31, 2023Updated 2 years ago
- Infering ancestral synteny with hierarchical orthologous groups☆38Oct 17, 2025Updated 5 months ago
- Differential quantification of alternative splicing events on spliced pangenome graphs☆15Jan 30, 2026Updated last month
- HitSV: Maximizing discovery of structural variants across sequencing technologies☆26Feb 18, 2026Updated last month
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆36Oct 29, 2025Updated 4 months ago