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@algbio

Algorithmic Bioinformatics Group @ University of Helsinki

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  1. ggcat ggcat Public

    Compacted and colored de Bruijn graph construction and querying

    Rust 78 10

  2. themisto themisto Public

    Space-efficient pseudoalignment with a colored de Bruijn graph

    C++ 52 4

  3. GraphChainer GraphChainer Public

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

    C++ 32 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++ 23 6

  5. matchtigs matchtigs Public

    Minimum plain text representation of kmer sets

    Rust 17 5

  6. emerald emerald Public

    EMERALD calculates safety-windows by exploring the suboptimal alignment space

    C++ 16

Repositories

Showing 10 of 39 repositories
  • SBWT Public

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

    algbio/SBWT’s past year of commit activity
    C++ 23 GPL-2.0 6 0 0 Updated Dec 20, 2024
  • optimized-fd Public
    algbio/optimized-fd’s past year of commit activity
    Python 2 MIT 0 0 0 Updated Dec 20, 2024
  • Badger Public

    Badger is a long read barcode calling tool

    algbio/Badger’s past year of commit activity
    Python 2 GPL-2.0 0 0 0 Updated Dec 19, 2024
  • ggcat Public

    Compacted and colored de Bruijn graph construction and querying

    algbio/ggcat’s past year of commit activity
    Rust 78 MIT 10 7 0 Updated Dec 18, 2024
  • themisto Public

    Space-efficient pseudoalignment with a colored de Bruijn graph

    algbio/themisto’s past year of commit activity
    C++ 52 GPL-2.0 4 12 1 Updated Dec 9, 2024
  • SRFAligner Public
    algbio/SRFAligner’s past year of commit activity
    C++ 13 0 2 0 Updated Dec 5, 2024
  • founderblockgraphs Public

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

    algbio/founderblockgraphs’s past year of commit activity
    C++ 3 GPL-3.0 1 1 0 Updated Nov 15, 2024
  • algbio/safe-sequences’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Nov 4, 2024
  • efg-mems Public

    MEM finding on (elastic founder) graphs

    algbio/efg-mems’s past year of commit activity
    C++ 1 GPL-2.0 0 0 0 Updated Oct 27, 2024
  • matchtigs Public

    Minimum plain text representation of kmer sets

    algbio/matchtigs’s past year of commit activity
    Rust 17 BSD-2-Clause 5 0 0 Updated Sep 19, 2024

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