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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

    Rust 942 192

  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 220 26

  3. oarfish oarfish Public

    long read RNA-seq quantification

    Rust 127 8

  4. pufferfish pufferfish Public

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

    C 113 22

  5. cuttlefish cuttlefish Public

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

    Rust 101 14

  6. RapMap RapMap Public

    Rapid sensitive and accurate read mapping via quasi-mapping

    C++ 90 23

Repositories

Showing 10 of 146 repositories
  • piscem-rs Public
    COMBINE-lab/piscem-rs's past year of commit activity
    Rust 15 BSD-3-Clause 2 1 1 Updated Nov 1, 2026
  • salmon Public

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

    COMBINE-lab/salmon's past year of commit activity
    Rust 942 BSD-3-Clause 192 383 10 Updated Nov 1, 2026
  • ksw2rs Public

    a native rust port of the KSW2 alignment procedure

    COMBINE-lab/ksw2rs's past year of commit activity
    Rust 5 BSD-3-Clause 3 0 0 Updated Nov 1, 2026
  • piscem-infer Public
    COMBINE-lab/piscem-infer's past year of commit activity
    Rust 15 BSD-3-Clause 1 0 0 Updated Oct 31, 2026
  • piscem Public

    Mapping sequencing data to De Bruijn graphs, fast

    COMBINE-lab/piscem's past year of commit activity
    Rust 39 BSD-3-Clause 3 2 0 Updated Oct 31, 2026
  • libradicl Public
    COMBINE-lab/libradicl's past year of commit activity
    Rust 5 BSD-3-Clause 2 6 0 Updated Oct 31, 2026
  • sshash-rs Public

    A Rust implementation of SSHash

    COMBINE-lab/sshash-rs's past year of commit activity
    Rust 20 BSD-3-Clause 3 1 0 Updated Oct 30, 2026
  • cf1-rs Public

    An subset of Cuttlefish 1, rewritten in Rust, to provide maximal unitigs and tiling information for piscem indexing.

    COMBINE-lab/cf1-rs's past year of commit activity
    Rust 2 BSD-3-Clause 0 0 0 Updated Oct 30, 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 220 BSD-3-Clause 26 25 2 Updated Oct 29, 2026
  • combine-lab.github.io Public
    COMBINE-lab/combine-lab.github.io's past year of commit activity
    HTML 12 15 1 1 Updated Oct 27, 2026
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