egonelbre / fm-indexLinks
Educational implementation of BWT and FM-index
☆57Updated 6 years ago
Alternatives and similar repositories for fm-index
Users that are interested in fm-index are comparing it to the libraries listed below
Sorting:
- Incremental construction of FM-index for DNA sequences☆72Updated last year
- deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph☆30Updated 4 years ago
- Fast and accurate set similarity estimation via containment min hash☆42Updated last year
- A fast, AVX2 and ARM Neon accelerated FM index library☆34Updated 9 months ago
- A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes☆74Updated last year
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆55Updated last year
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆52Updated last year
- An Oxford Nanopore Basecaller☆70Updated 4 years ago
- Substring index for paths in a graph☆60Updated 5 months ago
- Streaming algorithm for computing kmer statistics for massive genomics datasets☆54Updated 5 years ago
- Naive de Bruijn graph implementation in python☆37Updated 7 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 4 years ago
- BWT-based index for graphs☆72Updated 6 months ago
- REINDEER REad Index for abuNDancE quERy☆56Updated 2 months ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Updated 6 months ago
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 5 years ago
- Code accompanying the publication for compressed graph annotation☆13Updated 6 years ago
- Smith-Waterman database searches with inter-sequence SIMD parallelisation☆60Updated last year
- Bioinformatics Open Source Sequence machine☆32Updated 2 years ago
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Updated 7 months ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆66Updated last year
- pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)☆49Updated 8 years ago
- 1-code framework: docs, C-library, and tools☆22Updated last month
- Enhanced Artificial Genome Engine: next generation sequencing reads simulator☆33Updated 5 years ago
- URMAP ultra-fast read mapper☆38Updated 5 years ago
- a string to graph aligner☆41Updated 9 years ago
- online notebooks for a review of genome sketching☆60Updated 5 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 3 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆109Updated 11 months ago
- Parallel Sequence to Graph Alignment☆36Updated 2 years ago