A list of software for pangenomics
☆200Sep 16, 2026Updated last month
Alternatives and similar repositories for awesome-pangenomes
Users that are interested in awesome-pangenomes are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers☆25Feb 16, 2026Updated 8 months ago
- Panacus is a tool for computing statistics for GFA-formatted pangenome graphs☆139Sep 8, 2026Updated last month
- Pangenome graphs visualisation, distance computing, reconstruction of sequences and other utility functions☆38Apr 28, 2026Updated 5 months ago
- the pangenome graph builder☆519Jul 24, 2026Updated 2 months ago
- an interactive visualization and interpretation framework of reference-projected pangenome graphs☆42Feb 15, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Pangenome-based genome inference☆181Sep 15, 2026Updated last month
- Identification of transposable element families from pangenome polymorphisms☆57Aug 11, 2026Updated 2 months ago
- Constructing a pangenome gene graph☆212Aug 11, 2025Updated last year
- Mumemto: multi-MUM and MEM finding across pangenomes☆139Sep 21, 2026Updated 3 weeks ago
- COsine SImilarity-based Genotyper using pangenomes☆40Sep 24, 2026Updated 3 weeks ago
- LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads☆111Jun 25, 2026Updated 3 months ago
- Show pangenome graphs in an easy way☆61Aug 7, 2025Updated last year
- ☆32Oct 7, 2026Updated last week
- GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered …☆277Oct 6, 2026Updated last week
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Pairwise whole genome aligner☆244Sep 4, 2026Updated last month
- implicit pangenome graph☆114Updated this week
- 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
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆15Apr 28, 2026Updated 5 months ago
- Synteny and Rearrangement Identifier☆496Jul 1, 2026Updated 3 months ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆225Sep 28, 2026Updated 2 weeks ago
- This is the standalone version of the EviAnn pipeline☆187Oct 7, 2026Updated last week
- Statistics and analysis for variation graphs☆56Dec 17, 2024Updated last year
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 3 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆251Sep 16, 2026Updated last month
- ☆52Jun 27, 2026Updated 3 months ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆47Oct 13, 2024Updated 2 years ago
- plane sweep filtering genome alignments☆24Sep 28, 2026Updated 2 weeks ago
- HELIANO is a software for detection and classification of Helitron-like elements.☆35Jul 13, 2026Updated 3 months ago
- Tools for manipulating sequence graphs in the GFA and rGFA formats☆254Dec 16, 2025Updated 10 months ago
- This repository contains relevant code and explanation for ”Leveraging a phased pangenome to design ideal haplotypes for hybrid potato br…☆40Oct 29, 2025Updated 11 months ago
- Genome Assembly 102☆19Apr 23, 2025Updated last year
- ☆166Apr 13, 2026Updated 6 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- High-precision TE Annotator☆168Dec 4, 2025Updated 10 months ago
- An accurate GFF3/GTF lift over pipeline☆561Aug 1, 2023Updated 3 years ago
- Official home of genome aligner based upon notion of Cactus graphs☆714Updated this week
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆421Aug 25, 2026Updated last month
- Evaluation and polishing workflows for T2T genome assemblies☆174Sep 15, 2026Updated last month
- Long read aligner for cyclic and acyclic pangenome graphs☆41Dec 20, 2023Updated 2 years ago
- ☆24May 31, 2024Updated 2 years ago