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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++ 854 183

  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 198 19

  3. pufferfish pufferfish Public

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

    C 111 22

  4. oarfish oarfish Public

    long read RNA-seq quantification

    Rust 99 6

  5. cuttlefish cuttlefish Public

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

    C++ 92 13

  6. RapMap RapMap Public

    Rapid sensitive and accurate read mapping via quasi-mapping

    C++ 90 23

Repositories

Showing 10 of 129 repositories
  • prep_reads Public

    simple and dirty internal tool for putting simulated reads into the right format for downstream consumption

    COMBINE-lab/prep_reads’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Jan 17, 2026
  • seqproc Public
    COMBINE-lab/seqproc’s past year of commit activity
    Rust 4 BSD-3-Clause 1 4 0 Updated Jan 15, 2026
  • mim Public

    A small, auxiliary index to massively improve parallel fastq parsing

    COMBINE-lab/mim’s past year of commit activity
    C++ 30 BSD-3-Clause 1 3 0 Updated Jan 13, 2026
  • 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 1 Updated Jan 9, 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 198 BSD-3-Clause 19 24 0 Updated Jan 9, 2026
  • oarfish Public

    long read RNA-seq quantification

    COMBINE-lab/oarfish’s past year of commit activity
    Rust 99 BSD-3-Clause 6 8 1 Updated Jan 9, 2026
  • ANTISEQUENCE Public Forked from noahcape/ANTISEQUENCE

    Rust library for processing sequencing reads.

    COMBINE-lab/ANTISEQUENCE’s past year of commit activity
    Rust 0 MIT 4 0 0 Updated Jan 2, 2026
  • QCatch Public

    Quality Control downstream of alevin-fry / simpleaf

    COMBINE-lab/QCatch’s past year of commit activity
    HTML 5 1 0 1 Updated Dec 29, 2025
  • libradicl Public
    COMBINE-lab/libradicl’s past year of commit activity
    Rust 5 BSD-3-Clause 2 1 0 Updated Dec 23, 2025
  • COMBINE-lab/combine-lab.github.io’s past year of commit activity
    HTML 13 11 1 1 Updated Dec 8, 2025

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