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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++ 750 159

  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 157 15

  3. pufferfish pufferfish Public

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

    C 107 19

  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++ 75 7

  6. terminus terminus Public

    Rust 57 4

Repositories

Showing 10 of 114 repositories
  • simpleaf Public

    A rust framework to make using alevin-fry even simpler

    COMBINE-lab/simpleaf’s past year of commit activity
    Rust 44 BSD-3-Clause 3 7 0 Updated Jul 16, 2024
  • piscem Public

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

    COMBINE-lab/piscem’s past year of commit activity
    Rust 19 BSD-3-Clause 1 5 0 Updated Jul 16, 2024
  • cuttlefish Public

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

    COMBINE-lab/cuttlefish’s past year of commit activity
    C++ 75 BSD-3-Clause 7 10 2 Updated Jul 16, 2024
  • roers Public
    COMBINE-lab/roers’s past year of commit activity
    Rust 3 BSD-3-Clause 1 0 1 Updated Jul 12, 2024
  • 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 157 BSD-3-Clause 15 18 0 Updated Jul 12, 2024
  • libradicl Public
    COMBINE-lab/libradicl’s past year of commit activity
    Rust 1 BSD-3-Clause 2 0 0 Updated Jul 12, 2024
  • grangers Public
    COMBINE-lab/grangers’s past year of commit activity
    Rust 16 BSD-3-Clause 1 0 0 Updated Jul 7, 2024
  • 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 0 1 0 Updated Jul 2, 2024
  • kmers Public

    A bit-packed k-mer representation (and relevant utilities) for rust

    COMBINE-lab/kmers’s past year of commit activity
    Rust 47 BSD-3-Clause 10 7 1 Updated Jun 26, 2024
  • RapClust Public

    Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes

    COMBINE-lab/RapClust’s past year of commit activity
    Python 30 6 6 1 Updated Jun 16, 2024
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