Algorithmic Bioinformatics Lab @ University of Helsinki

Helsinki, Finland

Pinned Repositories

emerald
EMERALD calculates safety-windows by exploring the suboptimal alignment space
Language:C++17 4 10
ggcat
Compacted and colored de Bruijn graph construction and querying
Language:Rust84 5 4612
GraphChainer
An accurate aligner of long reads to a variation graph, based on co-linear chaining
Language:C++33 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 Notebook14 5 10
PerformanceMPC
Efficient C++ implementations of different fast algorithms for Minimum Path Cover
Language:C++7 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++24 6 46
SRFAligner
Language:C++13 5 20
themisto
Space-efficient pseudoalignment with a colored de Bruijn graph
Language:C++53 7 284

Algorithmic Bioinformatics Lab @ University of Helsinki's Repositories

algbio/ggcat
Compacted and colored de Bruijn graph construction and querying
Language:Rust84 5 4612
algbio/themisto
Space-efficient pseudoalignment with a colored de Bruijn graph
Language:C++53 7 284
algbio/GraphChainer
An accurate aligner of long reads to a variation graph, based on co-linear chaining
Language:C++33 4 64
algbio/SBWT
Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)
Language:C++24 6 46
algbio/emerald
EMERALD calculates safety-windows by exploring the suboptimal alignment space
Language:C++17 4 10
algbio/matchtigs
Minimum plain text representation of kmer sets
Language:Rust17 6 45
algbio/MFD-ILP
Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.
Language:Jupyter Notebook14 5 10
algbio/SRFAligner
Language:C++13 5 20
algbio/flowpaths
A Python package to quickly decompose weighted graphs into weights paths, under various models.
Language:Python71
algbio/PerformanceMPC
Efficient C++ implementations of different fast algorithms for Minimum Path Cover
Language:C++7 2 03
algbio/spl-IsoQuant
A pipeline for processing Spl-Iso-Seq data
Language:Python6 4 30
algbio/mfd-safety
Language:Python4 3 00
algbio/practical-omnitigs
A repository to conduct experiments with omnitig-related models for genome assembly.
Language:Jupyter Notebook4 4 1080
algbio/emerald-analysis
Language:Jupyter Notebook3 4 00
algbio/founderblockgraphs
Constructs segment repeat-free founder block graphs from multiple sequence alignments
Language:C++3 8 101
algbio/Badger
Badger is a long read barcode calling tool
Language:Python2 5 0
algbio/optimized-fd
Language:Python2 5 10
algbio/RobustFlowDecomposition
Flow Decomposition Under Uncertainty
Language:Python2 1 01
algbio/alignment-safety
Language:Jupyter Notebook1 6 00
algbio/anchors-in-chaining
Language:Python1 4 0
algbio/br-index-mems
MEM finding on texts and graphs using bidirectional r-index
Language:C++1 0 01
algbio/efg-mems
MEM finding on (elastic founder) graphs
Language:C++1 5 10
algbio/panvc-founders
Instructions and examples for using PanVC with founder sequences
Language:Python1 6 0
algbio/panvc3-experiments
Experiments for evaluating PanVC 3
Language:Python1 5 0
algbio/safe-sequences
Language:Python10
algbio/flowtigs
Language:Rust4 0
algbio/GraphChainer-scripts
Language:Python3 0
algbio/KMC
A fork of KMC used in the SBWT repository https://github.com/algbio/SBWT
Language:C++0 04
algbio/panvc-sample-workflow
Sample variant calling workflow using short reads for PanVC
Language:Python6 0
algbio/sdsl-lite
Fork of Succinct Data Structure Library 2.0 used in Themisto
Language:C++0 0