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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++ 876 184

  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 203 20

  3. pufferfish pufferfish Public

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

    C 112 22

  4. oarfish oarfish Public

    long read RNA-seq quantification

    Rust 109 8

  5. cuttlefish cuttlefish Public

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

    C++ 91 12

  6. RapMap RapMap Public

    Rapid sensitive and accurate read mapping via quasi-mapping

    C++ 90 23

Repositories

Showing 10 of 137 repositories
  • seqproc Public
    COMBINE-lab/seqproc’s past year of commit activity
    Rust 4 BSD-3-Clause 1 4 1 Updated Apr 16, 2026
  • simpleaf Public

    A rust framework to make using alevin-fry even simpler

    COMBINE-lab/simpleaf’s past year of commit activity
    Rust 64 BSD-3-Clause 6 17 0 Updated Apr 15, 2026
  • piscem Public

    Mapping sequencing data to De Bruijn graphs, fast

    COMBINE-lab/piscem’s past year of commit activity
    Rust 32 BSD-3-Clause 3 2 0 Updated Apr 15, 2026
  • piscem-rs Public
    COMBINE-lab/piscem-rs’s past year of commit activity
    Rust 5 1 0 0 Updated Apr 15, 2026
  • sshash-rs Public

    A Rust implementation of SSHash

    COMBINE-lab/sshash-rs’s past year of commit activity
    Rust 16 BSD-3-Clause 1 1 0 Updated Apr 15, 2026
  • 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 203 BSD-3-Clause 20 24 0 Updated Apr 15, 2026
  • piscem-infer Public
    COMBINE-lab/piscem-infer’s past year of commit activity
    Rust 15 BSD-3-Clause 1 0 0 Updated Mar 27, 2026
  • 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 2 0 Updated Mar 23, 2026
  • libradicl Public
    COMBINE-lab/libradicl’s past year of commit activity
    Rust 5 BSD-3-Clause 2 1 0 Updated Mar 21, 2026
  • grangers Public
    COMBINE-lab/grangers’s past year of commit activity
    Rust 19 BSD-3-Clause 2 0 0 Updated Mar 19, 2026

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