BWT-based index for graphs
☆73Mar 12, 2025Updated last year
Alternatives and similar repositories for gcsa2
Users that are interested in gcsa2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Substring index for paths in a graph☆60Mar 28, 2026Updated last month
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 5 months ago
- Relative data structures based on the BWT☆12Apr 28, 2018Updated 8 years ago
- A succinct colored dBG representation☆12Sep 11, 2018Updated 7 years ago
- Run-length compressed BWT with LZ77 sampled suffix array☆10Apr 25, 2022Updated 4 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A tool for merging large BWTs☆23Nov 26, 2020Updated 5 years ago
- deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph☆31Jan 19, 2021Updated 5 years ago
- EXPERIMENTAL implementation of side graph☆10Apr 16, 2015Updated 11 years ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Mar 12, 2024Updated 2 years ago
- This repo is deprecated. Please use gfatools instead.☆15Aug 17, 2018Updated 7 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated last year
- GBWT-based handle graph☆33May 15, 2026Updated last week
- Population Reference Graphs for the HLA and MHC.☆35Dec 18, 2018Updated 7 years ago
- Graphical Fragment Assembly (GFA) Format Specification☆219Aug 21, 2024Updated last year
- 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.
- Tool (experimental) to compute layout from overlaps with spectral algorithm☆11Nov 28, 2017Updated 8 years ago
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Jun 4, 2022Updated 3 years ago
- C++ library for analysing and storing large-scale cohorts of sequence variant data☆17Aug 27, 2019Updated 6 years ago
- BWT Text Indexing Library: a set of tools to work with BWT-based text indexes☆25Apr 25, 2022Updated 4 years ago
- StriDe Assembler☆25Nov 23, 2017Updated 8 years ago
- VariantStore: A Large-Scale Genomic Variant Search Index☆40Jul 9, 2021Updated 4 years ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆118Dec 13, 2024Updated last year
- compacted de Bruijn graph construction in low memory☆100Nov 4, 2025Updated 6 months ago
- BlastGraph is a new tool for computing intensive approximate pattern matching in a sequence graph or a de-Bruijn graph. Given an oriented…☆12May 9, 2013Updated 13 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- alignment to variation graph inducer☆159Apr 11, 2026Updated last month
- succinct labeled graphs with collections and paths☆15Nov 18, 2018Updated 7 years ago
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆55May 17, 2022Updated 4 years ago
- Pan-genome Seed Index☆20Mar 12, 2025Updated last year
- de Bruijn Graph-based read aligner☆36Sep 3, 2018Updated 7 years ago
- tools for working with genome variation graphs☆1,320Updated this week
- Code to create a PRG from a Multiple Sequence Alignment file☆25Sep 10, 2025Updated 8 months ago
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- 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.
- SeqOthello supports fast coverage query and containment query.☆12May 8, 2019Updated 7 years ago
- De novo genome assembly and multisample variant calling☆112Mar 28, 2019Updated 7 years ago
- Online material and code base for the article Coordinates and Intervals in Graph Based Reference Genomes☆11May 2, 2017Updated 9 years ago
- compressed, queryable variation graphs☆11Jun 25, 2015Updated 10 years ago
- Practical Dynamic de Bruijn Graphs☆18Oct 1, 2020Updated 5 years ago
- base-accurate DNA sequence alignments using edlib and mashmap2☆32Feb 15, 2021Updated 5 years ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24May 30, 2024Updated last year