Algorithmic Bioinformatics Lab @ University of Helsinki

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48 repositories

flowpaths
Public
A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models.
bioinformatics graph-algorithms network-analysis
bioinformatics graph-algorithms network-analysis bioinformatics-analysis flows integer-linear-programming flow-decomposition network-flows
Python
•
MIT License
•6•12•0•1•Updated Mar 10, 2026Mar 10, 2026
ggcat
Public
Compacted and colored de Bruijn graph construction and querying
rust bioinformatics sequencing
rust bioinformatics sequencing bioinformatics-pipeline genome-assembly de-novo-assembly debruijn-graph
Rust
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MIT License
•14•94•8•1•Updated Mar 6, 2026Mar 6, 2026
spl-IsoQuant
Public
A pipeline for processing single-cell and spatial long-read transcriptomic data
nanopore pacbio single-cell
nanopore pacbio single-cell isoform-quantification spatial-transcriptomics long-read-sequencing single-cell-transcriptomics
Python
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Other
•0•9•5•0•Updated Mar 6, 2026Mar 6, 2026
BubbleFinder
Public
Find and decompose genomic variation sites in pangenome graphs
C++
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GNU General Public License v3.0
•1•10•0•0•Updated Mar 4, 2026Mar 4, 2026
emerald-ui
Public
Interactive Protein Sequence Alignment Visualization
protein-structure edit-distance alignment
protein-structure edit-distance alignment safety protein-sequences uniprot blosum-matrix swissprot alphafold molstar
TypeScript
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MIT License
•1•4•0•0•Updated Feb 26, 2026Feb 26, 2026
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.8k•0•0•0•Updated Jan 23, 2026Jan 23, 2026
BubbleFinder-experiments
Public
Python
•1•0•0•0•Updated Jan 22, 2026Jan 22, 2026
practical-omnitigs
Public
A repository to conduct experiments with omnitig-related models for genome assembly.
genome-assembly omnitigs
genome-assembly omnitigs
Jupyter Notebook
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BSD 2-Clause "Simplified" License
•0•4•13•0•Updated Jan 14, 2026Jan 14, 2026
emerald
Public
EMERALD calculates safety-windows by exploring the suboptimal alignment space
protein-structure sequence-alignment
protein-structure sequence-alignment
C++
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GNU General Public License v3.0
•0•17•1•0•Updated Jan 13, 2026Jan 13, 2026
eds
Public
Constructing EDSes from MSAs
C++
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GNU General Public License v2.0
•0•0•0•0•Updated Dec 29, 2025Dec 29, 2025
SRFAligner
Public
C++
•0•13•1•0•Updated Dec 26, 2025Dec 26, 2025
MFD-ILP
Public
Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.
Jupyter Notebook
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MIT License
•0•14•0•0•Updated Dec 4, 2025Dec 4, 2025
safe-sequences
Public
Python
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GNU General Public License v3.0
•0•1•0•0•Updated Dec 1, 2025Dec 1, 2025
RobustFlowDecomposition
Public
Flow Decomposition Under Uncertainty
Python
•2•2•0•0•Updated Nov 25, 2025Nov 25, 2025
optimized-fd
Public
Python
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MIT License
•0•2•0•0•Updated Nov 25, 2025Nov 25, 2025
GraphChainer-scripts
Public
Python
•0•1•1•0•Updated Nov 13, 2025Nov 13, 2025
flow-datasets
Public
A collection of flow networks constructed from bacterial genomes and viral strains
Python
•0•0•0•0•Updated Nov 11, 2025Nov 11, 2025
ChainX
Public
Anchor chaining method for nucleotide sequences
C++
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Apache License 2.0
•4•3•0•0•Updated Aug 6, 2025Aug 6, 2025
founderblockgraphs
Public
Constructs segment repeat-free founder block graphs from multiple sequence alignments
C++
•
GNU General Public License v3.0
•1•4•1•0•Updated Jul 16, 2025Jul 16, 2025
Badger
Public
Badger is a long read barcode calling tool
Python
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GNU General Public License v2.0
•0•2•0•0•Updated Jul 10, 2025Jul 10, 2025
GraphChainer
Public
An accurate aligner of long reads to a variation graph, based on co-linear chaining
read-aligners variation-graph pangenomics
read-aligners variation-graph pangenomics long-reads
C++
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MIT License
•4•35•2•0•Updated May 23, 2025May 23, 2025
themisto
Public
Space-efficient pseudoalignment with a colored de Bruijn graph
C++
•
GNU General Public License v2.0
•4•52•13•1•Updated Mar 13, 2025Mar 13, 2025
SBWT
Public
Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)
indexing bwt k-mers
indexing bwt k-mers
C++
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GNU General Public License v2.0
•6•24•0•0•Updated Mar 13, 2025Mar 13, 2025
KMC
Public
A fork of KMC used in the SBWT repository https://github.com/algbio/SBWT
C++
•83•0•0•2•Updated Mar 13, 2025Mar 13, 2025
matchtigs
Public
Minimum plain text representation of kmer sets
Rust
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BSD 2-Clause "Simplified" License
•5•16•0•0•Updated Jan 30, 2025Jan 30, 2025
efg-mems
Public
MEM finding on (elastic founder) graphs
C++
•
GNU General Public License v2.0
•0•1•0•0•Updated Oct 27, 2024Oct 27, 2024
panvc3-experiments
Public
Experiments for evaluating PanVC 3
Python
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MIT License
•0•1•0•0•Updated Sep 13, 2024Sep 13, 2024
panvc-sample-workflow
Public
Sample variant calling workflow using short reads for PanVC
Python
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MIT License
•0•0•0•0•Updated Aug 15, 2024Aug 15, 2024
flowtigs
Public
Rust
•
BSD 2-Clause "Simplified" License
•0•1•0•0•Updated Aug 9, 2024Aug 9, 2024
emerald-analysis
Public
Jupyter Notebook
•0•3•0•0•Updated Dec 14, 2023Dec 14, 2023