Algorithmic Bioinformatics Group @ University of Helsinki

Helsinki, Finland

Pinned Repositories

emerald
EMERALD calculates safety-windows by exploring the suboptimal alignment space
Language:C++16 4 10
ggcat
Compacted and colored de Bruijn graph construction and querying
Language:Rust73 6 3610
GraphChainer
An accurate aligner of long reads to a variation graph, based on co-linear chaining
Language:C++30 4 64
matchtigs
Minimum plain text representation of kmer sets
Language:Rust17 6 45
metaflow
MetaFlow is a program for community profiling of a metagenomic sample
Language:C++7 2 31
MFD-ILP
Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.
Language:Jupyter Notebook12 5 10
PerformanceMPC
Efficient C++ implementations of different fast algorithms for Minimum Path Cover
Language:C++5 2 03
SBWT
Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)
Language:C++23 6 46
themisto
Space-efficient pseudoalignment with a colored de Bruijn graph
Language:C++50 7 284
VOMM
Space-efficient variable-order Markov models
Language:C++5 6 00

algbio/metaflow
MetaFlow is a program for community profiling of a metagenomic sample
Language:C++7 2 31
algbio/VOMM
Space-efficient variable-order Markov models
Language:C++5 6 00
algbio/Introduction-to-Applied-Bioinformatics
Genome assembly - From theory to practice (and back)
3 5 00
algbio/bwtCluster
Space-efficient clustering for metagenomic reads
Language:C++1 6 0
algbio/bdbwt
Bidirectional Burrows-Wheeler index
Language:C++6 0
algbio/GreedySuperstring
Greedy space-efficient construction of short approximate superstrings
Language:C++7 0
algbio/teaching-materials
Teaching materials of the Algorithmic Bioinformatics Group @ University of Helsinki
5 11