Explore @algbio Open Source projects

Algorithmic Bioinformatics Group @ University of Helsinki (@algbio)

algbio

Stars
241
Global Org. Rank 35,980 (Top 12 %)
Registered about 4 years ago
Most used languages

C++
45.0 %

Python
30.0 %

Jupyter Notebook
15.0 %

Rust
10.0 %
Location 🇫🇮 Finland
Country Total Rank 643
Country Ranking

Rust
35

Jupyter Notebook
74

C++
85

Python
651

ggcat

Compacted and colored de Bruijn graph construction and querying

themisto

Space-efficient pseudoalignment with a colored de Bruijn graph

GraphChainer

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

SBWT

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

emerald

EMERALD calculates safety-windows by exploring the suboptimal alignment space

matchtigs

Minimum plain text representation of kmer sets

MFD-ILP

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

Jupyter Notebook

metaflow

MetaFlow is a program for community profiling of a metagenomic sample

VOMM

Space-efficient variable-order Markov models

mfd-safety

emerald-analysis

Jupyter Notebook

Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)

practical-omnitigs

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

Jupyter Notebook

PerformanceMPC

RobustFlowDecomposition

Flow Decomposition Under Uncertainty

anchors-in-chaining

panvc-founders

Instructions and examples for using PanVC with founder sequences

optimized-fd

bwtCluster

Space-efficient clustering for metagenomic reads

founderblockgraphs

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

panvc3-experiments

Experiments for evaluating PanVC 3