Martinsos / opal
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
☆38Updated last year
Alternatives and similar repositories for opal:
Users that are interested in opal are comparing it to the libraries listed below
- An efficient index for the colored, compacted, de Bruijn graph☆109Updated 6 months ago
- Bidirectional WFA (Paper)☆46Updated 11 months ago
- Adaptive semi-global banded alignment on string graphs☆66Updated 6 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆86Updated last week
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 4 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 3 years ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆51Updated last year
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆63Updated 10 months ago
- Efficient, parallel compression for terabyte-scale data☆43Updated 3 months ago
- Create Bloom filters for a given reference and then use it to categorize sequences☆76Updated 4 months ago
- A repository for generating strobemers and evalaution☆78Updated last year
- Self-contained, multi-threaded fasta/q parser☆43Updated 6 months ago
- C implementation of the Landau-Vishkin algorithm☆35Updated 3 years ago
- A fast constructor of the compressed de Bruijn graph from many genomes☆40Updated 2 months ago
- Pan-Genomic Matching Statistics☆52Updated last year
- Parallel Sequence to Graph Alignment☆35Updated 2 years ago
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆49Updated last week
- BWT construction and search☆112Updated last month
- Core library of the Genome Analysis Toolbox with de-Bruijn graph☆63Updated 2 months ago
- Estimating k-mer coverage histogram of genomics data☆78Updated last year
- ☆65Updated last year
- Python bindings to bwa mem☆32Updated 5 years ago
- GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…☆67Updated 2 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆48Updated 2 years ago
- A fast, AVX2 and ARM Neon accelerated FM index library☆32Updated 4 months ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- Substring index for paths in a graph☆60Updated last month
- Assembled Genomes Compressor☆161Updated 4 months ago
- REINDEER REad Index for abuNDancE quERy☆57Updated 8 months ago
- Squeakr: An Exact and Approximate k -mer Counting System☆85Updated last month