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Algorithmic Bioinformatics Group @ University of Helsinki (algbio)

Algorithmic Bioinformatics Group @ University of Helsinki

algbio

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Location:Helsinki, Finland

Home Page:www.helsinki.fi/algorithmic-bioinformatics

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Algorithmic Bioinformatics Group @ University of Helsinki's repositories

ggcat

Compacted and colored de Bruijn graph construction and querying

Language:RustLicense:MITStargazers:68Issues:5Issues:29

themisto

Space-efficient pseudoalignment with a colored de Bruijn graph

Language:C++License:GPL-2.0Stargazers:48Issues:7Issues:23

GraphChainer

An accurate aligner of long reads to a variation graph, based on co-linear chaining

Language:C++License:MITStargazers:25Issues:4Issues:6

SBWT

Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)

Language:C++License:GPL-2.0Stargazers:23Issues:6Issues:4

emerald

EMERALD calculates safety-windows by exploring the suboptimal alignment space

Language:C++License:GPL-3.0Stargazers:16Issues:4Issues:1

matchtigs

Minimum plain text representation of kmer sets

Language:RustLicense:BSD-2-ClauseStargazers:15Issues:6Issues:4

MFD-ILP

Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.

Language:Jupyter NotebookLicense:MITStargazers:11Issues:5Issues:1

VOMM

Space-efficient variable-order Markov models

Language:C++Stargazers:5Issues:6Issues:0

mfd-safety

Language:PythonLicense:GPL-3.0Stargazers:4Issues:3Issues:0

emerald-analysis

Language:Jupyter NotebookStargazers:3Issues:0Issues:0

Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)

Stargazers:3Issues:5Issues:0

PerformanceMPC

Language:C++License:GPL-3.0Stargazers:3Issues:0Issues:0

practical-omnitigs

A repository to conduct experiments with omnitig-related models for genome assembly.

Language:Jupyter NotebookLicense:BSD-2-ClauseStargazers:3Issues:5Issues:108

RobustFlowDecomposition

Flow Decomposition Under Uncertainty

Language:PythonStargazers:2Issues:0Issues:0

anchors-in-chaining

Language:PythonLicense:MITStargazers:1Issues:4Issues:0

br-index-mems

MEM finding on texts and graphs using bidirectional r-index

Language:C++Stargazers:1Issues:0Issues:0

founderblockgraphs

Constructs segment repeat-free founder block graphs from multiple sequence alignments

Language:C++License:GPL-3.0Stargazers:1Issues:8Issues:9

optimized-fd

Language:PythonStargazers:1Issues:0Issues:0

panvc-founders

Instructions and examples for using PanVC with founder sequences

Language:PythonLicense:MITStargazers:1Issues:6Issues:0

panvc3-experiments

Experiments for evaluating PanVC 3

Language:PythonLicense:MITStargazers:1Issues:0Issues:0

efg-mems

MEM finding on (elastic founder) graphs

Language:C++License:GPL-2.0Stargazers:0Issues:0Issues:0

bdbwt-mem-chaining

Language:C++Stargazers:0Issues:0Issues:0

flow-decomposition-safety

Language:PythonLicense:GPL-3.0Stargazers:0Issues:0Issues:0

GraphChainer-scripts

Language:PythonStargazers:0Issues:3Issues:0

GreedySuperstring

Greedy space-efficient construction of short approximate superstrings

Language:C++License:GPL-3.0Stargazers:0Issues:0Issues:0

KMC

A fork of KMC used in the SBWT repository https://github.com/algbio/SBWT

Language:C++Stargazers:0Issues:0Issues:0

panvc-sample-workflow

Sample variant calling workflow using short reads for PanVC

Language:PythonLicense:MITStargazers:0Issues:0Issues:0

SafePathsRNAPC

Language:ShellLicense:GPL-3.0Stargazers:0Issues:0Issues:0

sdsl-lite

Fork of Succinct Data Structure Library 2.0 used in Themisto

License:NOASSERTIONStargazers:0Issues:0Issues:0

teaching-materials

Teaching materials of the Algorithmic Bioinformatics Group @ University of Helsinki

Stargazers:0Issues:5Issues:1