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@algbio

Algorithmic Bioinformatics Lab @ University of Helsinki

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  1. ggcat ggcat Public

    Compacted and colored de Bruijn graph construction and querying

    Rust 95 14

  2. themisto themisto Public

    Space-efficient pseudoalignment with a colored de Bruijn graph

    C++ 53 4

  3. GraphChainer GraphChainer Public

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

    C++ 35 4

  4. SBWT SBWT Public

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

    C++ 24 6

  5. emerald emerald Public

    EMERALD calculates safety-windows by exploring the suboptimal alignment space

    C++ 17

  6. matchtigs matchtigs Public

    Minimum plain text representation of kmer sets

    Rust 16 5

Repositories

Showing 10 of 50 repositories
  • BubbleFinder Public

    Find and decompose genomic variation sites in pangenome graphs

    algbio/BubbleFinder’s past year of commit activity
    C++ 12 GPL-3.0 1 0 0 Updated Apr 19, 2026
  • spqr-rust Public
    algbio/spqr-rust’s past year of commit activity
    Rust 1 0 0 0 Updated Apr 19, 2026
  • eds Public

    Constructing EDSes from MSAs

    algbio/eds’s past year of commit activity
    C++ 0 GPL-2.0 0 0 0 Updated Apr 18, 2026
  • emerald-ui Public

    Interactive Protein Sequence Alignment Visualization

    algbio/emerald-ui’s past year of commit activity
    TypeScript 4 MIT 1 0 0 Updated Apr 17, 2026
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    algbio/bioconda-recipes’s past year of commit activity
    Shell 0 MIT 3,882 0 0 Updated Apr 16, 2026
  • algbio/BubbleFinder-experiments’s past year of commit activity
    Python 0 1 0 0 Updated Mar 30, 2026
  • tsalign Public

    A sequence-to-sequence aligner that accounts for template switches

    algbio/tsalign’s past year of commit activity
    Rust 1 1 23 0 Updated Mar 20, 2026
  • flowpaths Public

    A Python package to quickly decompose weighted graphs (acyclic or not) into weighted paths or walks, under various models.

    algbio/flowpaths’s past year of commit activity
    Python 12 MIT 6 0 1 Updated Mar 16, 2026
  • spl-IsoQuant Public

    A pipeline for processing single-cell and spatial long-read transcriptomic data

    algbio/spl-IsoQuant’s past year of commit activity
    Python 11 0 5 0 Updated Mar 13, 2026
  • ggcat Public

    Compacted and colored de Bruijn graph construction and querying

    algbio/ggcat’s past year of commit activity
    Rust 95 MIT 14 9 1 Updated Mar 6, 2026

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