tlemane / kmtricks
modular k-mer count matrix and Bloom filter construction for large read collections
☆78Updated 3 months ago
Alternatives and similar repositories for kmtricks:
Users that are interested in kmtricks are comparing it to the libraries listed below
- A repository for generating strobemers and evalaution☆77Updated 9 months ago
- Estimating k-mer coverage histogram of genomics data☆76Updated last year
- Compacted and colored de Bruijn graph construction and querying☆79Updated this week
- Pan-Genomic Matching Statistics☆48Updated 9 months ago
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆46Updated this week
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆52Updated 2 years ago
- An efficient index for the colored, compacted, de Bruijn graph☆108Updated 3 months ago
- Efficient, parallel compression for terabyte-scale data☆36Updated this week
- BWT construction and search☆108Updated 3 weeks ago
- alignment to variation graph inducer☆144Updated 3 months ago
- Hybrid error correction of long reads using colored de Bruijn graphs☆100Updated 3 months ago
- A tool for Racon polishing of miniasm assemblies☆73Updated 3 years ago
- a Bioinformatics Application for Navigating De novo Assembly Graphs Easily☆118Updated last month
- Detecting multi-genome synteny using minimizer graph mapping☆73Updated this week
- Aligns short reads using dynamic seed size with strobemers☆160Updated this week
- Bidirectional WFA (Paper)☆42Updated 8 months ago
- A fast K-mer counter for high-fidelity shotgun datasets☆123Updated 2 weeks ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆113Updated 4 months ago
- ☆61Updated last month
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 2 years ago
- REINDEER REad Index for abuNDancE quERy☆57Updated 5 months ago
- Classifier for metagenomic sequences using FM-index with run-block compressed BWT.☆52Updated 2 weeks ago
- linearize and simplify variation graphs using blocked partial order alignment☆57Updated 2 months ago
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆119Updated this week
- Assembled Genomes Compressor☆159Updated last month
- A bit-packed k-mer representation (and relevant utilities) for rust☆47Updated 6 months ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆63Updated 7 months ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆85Updated 2 months ago
- Gfapy: a flexible and extensible software library for handling sequence graphs in Python☆66Updated 2 months ago
- Substring index for paths in a graph☆60Updated this week