jeizenga / wfalm
Refinements of the WFA alignment algorithm with better complexity
☆26Updated 2 years ago
Alternatives and similar repositories for wfalm:
Users that are interested in wfalm are comparing it to the libraries listed below
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆23Updated 3 weeks ago
- Parallel Sequence to Graph Alignment☆35Updated 2 years ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24Updated 9 months ago
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 4 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- Benchmarking pairwise aligners☆36Updated last month
- A reimplementation of the WaveFront Alignment algorithm at low memory☆49Updated 10 months ago
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆49Updated 3 weeks ago
- C implementation of the Landau-Vishkin algorithm☆35Updated 2 years ago
- Efficient, parallel compression for terabyte-scale data☆40Updated 2 months ago
- Optimized sequence graph implementations for graph genomics☆34Updated 3 months ago
- GBWT in Rust☆43Updated this week
- genome variation graphs constructed from HLA GRCh38 ALTs☆23Updated 3 years ago
- ☆17Updated last year
- Space-efficient pseudoalignment with a colored de Bruijn graph☆53Updated last week
- ☆28Updated last year
- Iterate over minimizers of a DNA sequence☆28Updated 8 months ago
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.☆36Updated last week
- Pairwise nucleotide alignment benchmark of Rust bindings☆31Updated last year
- Wavefront alignment algorithm (WFA) in Golang☆30Updated 4 months ago
- GBWT-based handle graph☆31Updated last week
- Bidirectional WFA (Paper)☆45Updated 10 months ago
- Snakemake pipeline for benchmarking read mappers☆16Updated last year
- GFA insert into GenomicSQLite☆49Updated 3 years ago
- Long read aligner for cyclic and acyclic pangenome graphs☆36Updated last year
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated 9 months ago
- An experimental tool to find approximate max-cuts in a large graph☆11Updated 3 years ago
- Contains the description of a file format to store kmers and associated values☆32Updated 2 years ago
- ☆25Updated 3 years ago
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆24Updated last week