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☆61Jul 7, 2026Updated 2 weeks ago
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 7 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
- GBWT-based handle graph☆35Jun 17, 2026Updated last month
- Genome inference from a population reference graph☆96Apr 1, 2025Updated last year
- Population Reference Graphs for the HLA and MHC.☆35Dec 18, 2018Updated 7 years ago
- An MPI Toolkit for large-scale genomic analysis☆16Feb 29, 2016Updated 10 years ago
- 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.
- Graphical Fragment Assembly (GFA) Format Specification☆221Aug 21, 2024Updated last year
- FM-index representation of a de Bruijn graph☆26Aug 7, 2017Updated 8 years ago
- Incremental construction of FM-index for DNA sequences☆72Jun 12, 2024Updated 2 years ago
- Tool (experimental) to compute layout from overlaps with spectral algorithm☆11Nov 28, 2017Updated 8 years ago
- C++ library for analysing and storing large-scale cohorts of sequence variant data☆17Aug 27, 2019Updated 6 years ago
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Jun 4, 2022Updated 4 years ago
- BWT Text Indexing Library: a set of tools to work with BWT-based text indexes☆25Apr 25, 2022Updated 4 years ago
- efficient alignment of strings to partially ordered string graphs☆33Apr 22, 2026Updated 3 months ago
- StriDe Assembler☆25Nov 23, 2017Updated 8 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- VariantStore: A Large-Scale Genomic Variant Search Index☆40Jul 9, 2021Updated 5 years ago
- de Bruijn Graph-based read aligner☆36Sep 3, 2018Updated 7 years ago
- alignment to variation graph inducer☆163Updated this week
- compacted de Bruijn graph construction in low memory☆101Nov 4, 2025Updated 8 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
- Pan-genome Seed Index☆20Jul 3, 2026Updated 3 weeks ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆56May 17, 2022Updated 4 years ago
- succinct labeled graphs with collections and paths☆15Nov 18, 2018Updated 7 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Online material and code base for the article Coordinates and Intervals in Graph Based Reference Genomes☆11May 2, 2017Updated 9 years ago
- tools for working with genome variation graphs☆1,328Updated this week
- Code to create a PRG from a Multiple Sequence Alignment file☆25Sep 10, 2025Updated 10 months ago
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- SeqOthello supports fast coverage query and containment query.☆12May 8, 2019Updated 7 years 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
- De novo genome assembly and multisample variant calling☆113Mar 28, 2019Updated 7 years ago