Algorithmic Bioinformatics Lab @ University of Helsinki

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42 repositories

flowpaths
Public
A Python package to quickly decompose weighted graphs into weights paths, under various models.
bioinformatics graph-algorithms network-analysis bioinformatics-analysis flows integer-linear-programming flow-decomposition network-flows
Python
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MIT License
•2•6•0•0•Updated Jun 18, 2025Jun 18, 2025
ggcat
Public
Compacted and colored de Bruijn graph construction and querying
rust bioinformatics sequencing bioinformatics-pipeline genome-assembly de-novo-assembly debruijn-graph
Rust
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MIT License
•12•83•6•0•Updated Jun 18, 2025Jun 18, 2025
emerald-ui
Public
TypeScript
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MIT License
•0•0•0•0•Updated Jun 17, 2025Jun 17, 2025
emerald
Public
EMERALD calculates safety-windows by exploring the suboptimal alignment space
protein-structure sequence-alignment
C++
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GNU General Public License v3.0
•0•17•1•0•Updated Jun 5, 2025Jun 5, 2025
spl-IsoQuant
Public
A pipeline for processing Spl-Iso-Seq data
Python
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Other
•0•2•0•0•Updated May 30, 2025May 30, 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 May 28, 2025May 28, 2025
GraphChainer
Public
An accurate aligner of long reads to a variation graph, based on co-linear chaining
read-aligners variation-graph pangenomics long-reads
C++
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MIT License
•4•32•2•0•Updated May 23, 2025May 23, 2025
founderblockgraphs
Public
Constructs segment repeat-free founder block graphs from multiple sequence alignments
C++
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GNU General Public License v3.0
•1•3•1•0•Updated May 9, 2025May 9, 2025
safe-sequences
Public
Python
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GNU General Public License v3.0
•0•1•0•0•Updated Apr 23, 2025Apr 23, 2025
GraphChainer-scripts
Public
Python
•0•0•1•1•Updated Apr 14, 2025Apr 14, 2025
SRFAligner
Public
C++
•0•13•1•0•Updated Apr 10, 2025Apr 10, 2025
ChainX
Public
Anchor chaining method for nucleotide sequences
C++
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Apache License 2.0
•3•0•0•0•Updated Apr 7, 2025Apr 7, 2025
themisto
Public
Space-efficient pseudoalignment with a colored de Bruijn graph
C++
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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
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++
•76•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•17•0•0•Updated Jan 30, 2025Jan 30, 2025
optimized-fd
Public
Python
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MIT License
•0•3•0•0•Updated Dec 24, 2024Dec 24, 2024
efg-mems
Public
MEM finding on (elastic founder) graphs
C++
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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
panvc-founders
Public
Instructions and examples for using PanVC with founder sequences
next-generation-sequencing variant-calling founder-sequences
Python
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MIT License
•0•1•0•0•Updated Nov 3, 2023Nov 3, 2023
br-index-mems
Public
MEM finding on texts and graphs using bidirectional r-index
C++
•3•1•0•0•Updated Oct 23, 2023Oct 23, 2023
practical-omnitigs
Public
A repository to conduct experiments with omnitig-related models for genome assembly.
genome-assembly omnitigs
Jupyter Notebook
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BSD 2-Clause "Simplified" License
•0•4•13•0•Updated Sep 15, 2023Sep 15, 2023
mfd-safety
Public
Python
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GNU General Public License v3.0
•0•4•0•0•Updated Aug 23, 2023Aug 23, 2023
anchors-in-chaining
Public
Python
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MIT License
•0•1•0•0•Updated Aug 11, 2023Aug 11, 2023
PerformanceMPC
Public
Efficient C++ implementations of different fast algorithms for Minimum Path Cover
reachability dag max-flow minimum-path-cover directed-acyclic-graph preflow antichains transitive-reduction min-flow path-cover
C++
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GNU General Public License v3.0
•3•7•0•0•Updated Aug 8, 2023Aug 8, 2023
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•13•1•0•Updated Jun 2, 2023Jun 2, 2023
RobustFlowDecomposition
Public
Flow Decomposition Under Uncertainty
Python
•2•2•0•0•Updated Apr 17, 2023Apr 17, 2023