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@COMBINE-lab

COMBINE lab

COMputational BIology and Network Evolution lab

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  1. salmon salmon Public

    🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

    C++ 807 167

  2. alevin-fry alevin-fry Public

    🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

    Rust 183 16

  3. pufferfish pufferfish Public

    An efficient index for the colored, compacted, de Bruijn graph

    C 110 21

  4. RapMap RapMap Public

    Rapid sensitive and accurate read mapping via quasi-mapping

    C++ 89 23

  5. cuttlefish cuttlefish Public

    Building the compacted de Bruijn graph efficiently from references or reads.

    C++ 87 11

  6. oarfish oarfish Public

    long read RNA-seq quantification

    Rust 85 5

Repositories

Showing 10 of 125 repositories
  • piscem Public

    Rust wrapper for the next generation (still currently in C++)

    COMBINE-lab/piscem’s past year of commit activity
    Rust 25 BSD-3-Clause 1 3 0 Updated May 31, 2025
  • piscem-cpp Public

    A small sparse and fast reference index based on SSHash and Tiling encoding

    COMBINE-lab/piscem-cpp’s past year of commit activity
    C 6 MIT 1 0 0 Updated May 31, 2025
  • QCatch Public

    Quality Control downstream of alevin-fry / simpleaf

    COMBINE-lab/QCatch’s past year of commit activity
    HTML 1 0 0 0 Updated May 30, 2025
  • alevin-fry Public

    🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

    COMBINE-lab/alevin-fry’s past year of commit activity
    Rust 183 BSD-3-Clause 16 21 0 Updated May 22, 2025
  • minspace Public
    COMBINE-lab/minspace’s past year of commit activity
    Rust 3 BSD-3-Clause 0 0 0 Updated May 12, 2025
  • oarfish Public

    long read RNA-seq quantification

    COMBINE-lab/oarfish’s past year of commit activity
    Rust 85 BSD-3-Clause 5 7 1 Updated May 5, 2025
  • cuttlefish Public

    Building the compacted de Bruijn graph efficiently from references or reads.

    COMBINE-lab/cuttlefish’s past year of commit activity
    C++ 87 BSD-3-Clause 11 18 1 Updated May 1, 2025
  • simpleaf Public

    A rust framework to make using alevin-fry even simpler

    COMBINE-lab/simpleaf’s past year of commit activity
    Rust 54 BSD-3-Clause 5 14 0 Updated Apr 29, 2025
  • af-anndata Public

    alevin-fry related processing of AnnData

    COMBINE-lab/af-anndata’s past year of commit activity
    Rust 0 BSD-3-Clause 0 1 0 Updated Apr 29, 2025
  • QCatch-resources Public
    COMBINE-lab/QCatch-resources’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Apr 14, 2025
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