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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++ 862 183

  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 201 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 104 8

  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 134 repositories
  • simpleaf Public

    A rust framework to make using alevin-fry even simpler

    COMBINE-lab/simpleaf’s past year of commit activity
    Rust 62 BSD-3-Clause 5 16 0 Updated Feb 24, 2026
  • piscem Public

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

    COMBINE-lab/piscem’s past year of commit activity
    Rust 30 BSD-3-Clause 2 3 0 Updated Feb 24, 2026
  • piscem-rs Public
    COMBINE-lab/piscem-rs’s past year of commit activity
    Rust 5 0 0 0 Updated Feb 24, 2026
  • QCatch Public

    Quality Control downstream of alevin-fry / simpleaf

    COMBINE-lab/QCatch’s past year of commit activity
    Python 5 2 0 2 Updated Feb 24, 2026
  • libradicl Public
    COMBINE-lab/libradicl’s past year of commit activity
    Rust 5 BSD-3-Clause 2 1 0 Updated Feb 23, 2026
  • sshash-rs Public

    A Rust implementation of SSHash

    COMBINE-lab/sshash-rs’s past year of commit activity
    Rust 13 BSD-3-Clause 0 0 0 Updated Feb 23, 2026
  • file-requirements Public

    build up collections of files to check their existence

    COMBINE-lab/file-requirements’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Feb 21, 2026
  • OUP-Bioinformatics-Typst Public

    Unofficial attempt at a Typst template for the Oxford Bioinformatics journal

    COMBINE-lab/OUP-Bioinformatics-Typst’s past year of commit activity
    Typst 3 BSD-3-Clause 0 0 0 Updated Feb 20, 2026
  • cuttlefish Public

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

    COMBINE-lab/cuttlefish’s past year of commit activity
    C++ 92 BSD-3-Clause 13 19 1 Updated Feb 20, 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 Feb 19, 2026

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