An accurate aligner of long reads to a variation graph, based on co-linear chaining
☆35May 23, 2025Updated last year
Alternatives and similar repositories for GraphChainer
Users that are interested in GraphChainer are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆13Dec 26, 2025Updated 5 months ago
- Long-read aligner to pangenome graphs☆29May 20, 2024Updated 2 years ago
- convert variation graph alignments to coverage maps over nodes☆27Jan 21, 2026Updated 4 months ago
- Long read aligner for cyclic and acyclic pangenome graphs☆41Dec 20, 2023Updated 2 years ago
- Identifying large scale inversions between two genomes by mapping genome 1's unique kmers onto genome 2.☆10Jun 6, 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.
- pangenome from maximal blocks in an MSA☆11Sep 17, 2024Updated last year
- ☆11Dec 9, 2022Updated 3 years ago
- ☆23Updated this week
- Rust implementation of Flavia95's GFAtoVCF☆16Jan 17, 2022Updated 4 years ago
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆37Apr 23, 2025Updated last year
- recompute GFA link overlaps☆26Sep 14, 2022Updated 3 years ago
- Utilities to detect and profile `het-kmers`☆12Aug 5, 2024Updated last year
- ☆15Jun 29, 2021Updated 4 years ago
- your friendly pangenome graph genotyper☆10Feb 6, 2023Updated 3 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Compares pangenome graphs by calculating the segmentation distance between two GFA (Graphical Fragment Assembly) files.☆13Apr 28, 2026Updated last month
- Optimal sequence-to-graph alignment with recombinations☆41Apr 28, 2026Updated last month
- A plant organellar Graphical Fragment Assembly toolkit☆16Sep 10, 2025Updated 8 months ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 7 months ago
- ☆21Feb 15, 2025Updated last year
- ☆19May 10, 2023Updated 3 years ago
- AlfaPang builds pangenome graphs without alignments or references.☆16Nov 7, 2025Updated 7 months ago
- strange cross-platform, performance-oriented and interactive pangenome and large graph visualization☆50Updated this week
- Unzip assembly graphs with Hi-C data and/or long reads.☆28May 7, 2026Updated last month
- 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.
- ☆29Aug 7, 2025Updated 10 months ago
- PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.☆19Apr 9, 2026Updated 2 months ago
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 7 months ago
- Compacted and colored de Bruijn graph construction and querying☆97Updated this week
- MEMO: MEM-based pangenome indexing for k-mer queries☆20Jun 11, 2024Updated last year
- Identification of transposable element families from pangenome polymorphisms☆56Jun 3, 2025Updated last year
- exploring viral genome assembly with variation graph tools☆20May 18, 2020Updated 6 years ago
- ☆287Dec 29, 2025Updated 5 months ago
- linearize and simplify variation graphs using blocked partial order alignment☆63Mar 31, 2026Updated 2 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.
- Kmer based genotyper for short reads.☆23Oct 19, 2021Updated 4 years ago
- General purpose utility related to GAF files☆29May 20, 2026Updated 2 weeks ago
- base-level dotplots from PAF alignments☆34Sep 18, 2025Updated 8 months ago
- Bifrost graph gene caller.☆98Apr 12, 2026Updated last month
- COsine SImilarity-based Genotyper using pangenomes☆36Updated this week
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 9 months ago
- implicit pangenome graph☆107Updated this week