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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- online variation graph induction☆12Oct 21, 2025Updated last year
- How many distinct k-mers are there in a sequence?☆11Feb 4, 2026Updated 8 months ago
- Population genetics analysis on VG☆17Apr 22, 2021Updated 5 years ago
- Differential k-mer analysis☆42Jan 29, 2024Updated 2 years ago
- ☆19May 10, 2023Updated 3 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated last year
- Clustering tool optimized for sparse distance matrices: ~16M elements with ~190M connections clustered in minutes.☆16Sep 12, 2026Updated last month
- extract MSAs from genome variation graphs☆34Mar 24, 2026Updated 7 months ago
- ☆21Nov 1, 2019Updated 6 years ago
- Importing vg json graphs to Python data structures.☆12Nov 11, 2020Updated 5 years ago
- Hidden Markov Model based Copy number caller☆20Jul 18, 2026Updated 3 months ago
- Population-scale detection of novel sequence insertions☆28Aug 16, 2022Updated 4 years ago
- nextflow parser☆10Feb 3, 2024Updated 2 years ago
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- convert variation graph alignments to coverage maps over nodes☆28Jan 21, 2026Updated 9 months ago
- A Python library for manipulation of CIGAR, MSA, and other alignment formats.☆12Apr 14, 2026Updated 6 months ago
- A Strategy for Building and Using a Human Reference Pangenome☆71May 29, 2020Updated 6 years ago
- NovoGraph: building whole genome graphs from long-read-based de novo assemblies☆46Feb 23, 2021Updated 5 years ago
- ☆32Dec 16, 2022Updated 3 years ago
- An experimental tool to estimate the similarity between all pairs of contigs☆40Apr 12, 2021Updated 5 years ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated last year
- A plant organellar Graphical Fragment Assembly toolkit☆17Oct 15, 2026Updated 2 weeks ago
- Code to create a PRG from a Multiple Sequence Alignment file☆26Sep 10, 2025Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- An accurate aligner of long reads to a variation graph, based on co-linear chaining☆35May 23, 2025Updated last year
- ☆13Jan 23, 2020Updated 6 years ago
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆38Apr 28, 2026Updated 6 months ago
- Pangenome graphs (review article on graph-based pangenomic methods)☆73Apr 15, 2020Updated 6 years ago
- Rust implementation of Flavia95's GFAtoVCF☆16Jan 17, 2022Updated 4 years ago
- KaryoScope: rapid, alignment-free sequence annotation for the pangenome era☆29Oct 21, 2026Updated last week
- the pangenome graph evaluator☆29Apr 12, 2021Updated 5 years ago
- exploring viral genome assembly with variation graph tools☆20May 18, 2020Updated 6 years ago
- GFA visualizer, GPU-accelerated using Vulkan☆80Aug 2, 2022Updated 4 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- Fast and accurate set similarity estimation via containment min hash☆41Jul 19, 2024Updated 2 years ago
- ☆15Mar 9, 2018Updated 8 years ago
- Identify differentially expressed k-mers between RNA-Seq datasets☆11Mar 1, 2021Updated 5 years ago
- Catalogue of pairwise alignment algorithms and benchmarks☆25Jan 6, 2026Updated 9 months ago
- in silico plasmid extraction☆13Sep 18, 2017Updated 9 years ago
- ☆46Jun 21, 2020Updated 6 years ago