A pipeline for making SWIft Genomes in a Graph (SWIGG) using k-mers
☆22Nov 22, 2019Updated 6 years ago
Alternatives and similar repositories for SWIGG
Users that are interested in SWIGG are comparing it to the libraries listed below
Sorting:
- Hidden Markov Model based Copy number caller☆20Dec 9, 2025Updated 3 months ago
- Population-scale detection of novel sequence insertions☆27Aug 16, 2022Updated 3 years ago
- Importing vg json graphs to Python data structures.☆12Nov 11, 2020Updated 5 years ago
- ☆19May 10, 2023Updated 2 years ago
- Population genetics analysis on VG☆17Apr 22, 2021Updated 4 years ago
- ☆15Jan 28, 2026Updated last month
- the pangenome graph evaluator☆29Apr 12, 2021Updated 4 years ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated 7 months ago
- ☆21Nov 1, 2019Updated 6 years ago
- For bluntifying overlapped GFAs☆13Jul 26, 2024Updated last year
- Differential k-mer analysis☆40Jan 29, 2024Updated 2 years ago
- mreps: software for tandem repeat identification in DNA☆15Nov 13, 2019Updated 6 years ago
- Code for building and testing variant ranking strategies☆17Aug 22, 2025Updated 6 months ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Add functional variant annotation to MAF file☆11Nov 20, 2024Updated last year
- extract MSAs from genome variation graphs☆34Mar 3, 2026Updated 2 weeks ago
- ☆46Jun 21, 2020Updated 5 years ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- Extracts subgraphs or components from a graph in GFA format☆24Nov 18, 2024Updated last year
- ☆13Jan 4, 2026Updated 2 months ago
- A read extraction and realignment tool for next generation sequencing data☆105Oct 29, 2022Updated 3 years ago
- ☆15Mar 9, 2018Updated 8 years ago
- Benchmarking variant calling in polyploids☆15Nov 26, 2021Updated 4 years ago
- NovoGraph: building whole genome graphs from long-read-based de novo assemblies☆46Feb 23, 2021Updated 5 years ago
- A Strategy for Building and Using a Human Reference Pangenome☆70May 29, 2020Updated 5 years ago
- ☆24Aug 25, 2025Updated 6 months ago
- ☆29Mar 27, 2024Updated last year
- Pangenome graphs (review article on graph-based pangenomic methods)☆72Apr 15, 2020Updated 5 years ago
- De Bruijn graph construction for large k.☆17Aug 31, 2021Updated 4 years ago
- A long-read analysis toolbox for cancer and population genomics☆23Jul 1, 2025Updated 8 months ago
- An experimental tool to estimate the similarity between all pairs of contigs☆40Apr 12, 2021Updated 4 years ago
- convert variation graph alignments to coverage maps over nodes☆27Jan 21, 2026Updated last month
- Reducing reference bias using multiple population reference genomes☆34May 27, 2024Updated last year
- Subclassification of disease states based on the intersection of literature and expression☆12Jan 15, 2019Updated 7 years ago
- Human pan-genome analysis pipeline☆31Apr 30, 2020Updated 5 years ago
- Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]☆11Mar 6, 2024Updated 2 years ago
- A fast, user-friendly analysis and evaluation toolkit for some DNA sequence classification tasks☆15Sep 22, 2018Updated 7 years ago
- Simulate mutations in genomes☆15Jun 15, 2020Updated 5 years ago
- Long read aligner for cyclic and acyclic pangenome graphs☆40Dec 20, 2023Updated 2 years ago