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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 70 11

  2. themisto themisto Public

    Space-efficient pseudoalignment with a colored de Bruijn graph

    C++ 49 3

  3. GraphChainer GraphChainer Public

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

    C++ 25 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 7

  5. matchtigs matchtigs Public

    Minimum plain text representation of kmer sets

    Rust 16 5

  6. emerald emerald Public

    EMERALD calculates safety-windows by exploring the suboptimal alignment space

    C++ 16

Repositories

Showing 10 of 35 repositories
  • founderblockgraphs Public

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

    algbio/founderblockgraphs’s past year of commit activity
    C++ 1 GPL-3.0 1 1 0 Updated Jun 26, 2024
  • spl-IsoQuant Public

    A pipeline for processing Spl-Iso-Seq data

    algbio/spl-IsoQuant’s past year of commit activity
    Python 1 0 0 0 Updated Jun 13, 2024
  • themisto Public

    Space-efficient pseudoalignment with a colored de Bruijn graph

    algbio/themisto’s past year of commit activity
    C++ 49 GPL-2.0 3 10 0 Updated Jun 12, 2024
  • Badger Public

    Badger is a long read barcode calling tool

    algbio/Badger’s past year of commit activity
    Python 0 GPL-2.0 0 0 0 Updated Jun 12, 2024
  • KMC Public Forked from refresh-bio/KMC

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

    algbio/KMC’s past year of commit activity
    C++ 0 73 0 2 Updated May 5, 2024
  • 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 7 0 0 Updated Apr 24, 2024
  • ggcat Public

    Compacted and colored de Bruijn graph construction and querying

    algbio/ggcat’s past year of commit activity
    Rust 70 MIT 11 9 1 Updated Mar 25, 2024
  • emerald Public

    EMERALD calculates safety-windows by exploring the suboptimal alignment space

    algbio/emerald’s past year of commit activity
    C++ 16 GPL-3.0 0 1 0 Updated Mar 15, 2024
  • efg-mems Public

    MEM finding on (elastic founder) graphs

    algbio/efg-mems’s past year of commit activity
    C++ 0 GPL-2.0 0 0 0 Updated Feb 16, 2024
  • algbio/optimized-fd’s past year of commit activity
    Python 1 0 0 0 Updated Feb 13, 2024

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