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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++ 782 164

  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 172 15

  3. pufferfish pufferfish Public

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

    C 108 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++ 84 9

  6. oarfish oarfish Public

    long read RNA-seq quantification

    Rust 73 3

Repositories

Showing 10 of 119 repositories
  • simpleaf Public

    A rust framework to make using alevin-fry even simpler

    COMBINE-lab/simpleaf’s past year of commit activity
    Rust 46 BSD-3-Clause 5 12 0 Updated Dec 11, 2024
  • libradicl Public
    COMBINE-lab/libradicl’s past year of commit activity
    Rust 1 BSD-3-Clause 2 0 0 Updated Dec 8, 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 172 BSD-3-Clause 15 20 0 Updated Dec 7, 2024
  • oarfish Public

    long read RNA-seq quantification

    COMBINE-lab/oarfish’s past year of commit activity
    Rust 73 BSD-3-Clause 3 3 1 Updated Nov 29, 2024
  • piscem Public

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

    COMBINE-lab/piscem’s past year of commit activity
    Rust 20 BSD-3-Clause 1 3 0 Updated Nov 27, 2024
  • COMBINE-lab/lr-rna-sim-scripts’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Nov 27, 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 1 1 0 Updated Nov 27, 2024
  • COMBINE-lab/alevin-fry-atac’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Nov 27, 2024
  • cuttlefish Public

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

    COMBINE-lab/cuttlefish’s past year of commit activity
    C++ 84 BSD-3-Clause 9 12 2 Updated Nov 14, 2024
  • seqcol_rs Public

    (unofficial) Rust implementation of SeqCol sequence collections

    COMBINE-lab/seqcol_rs’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Nov 14, 2024

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