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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++ 771 162

  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 165 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++ 79 8

  6. oarfish oarfish Public

    long read RNA-seq quantification

    Rust 66 2

Repositories

Showing 10 of 116 repositories
  • 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 Sep 18, 2024
  • oarfish Public

    long read RNA-seq quantification

    COMBINE-lab/oarfish’s past year of commit activity
    Rust 66 BSD-3-Clause 2 2 1 Updated Sep 4, 2024
  • seqproc Public
    COMBINE-lab/seqproc’s past year of commit activity
    Rust 4 BSD-3-Clause 1 4 0 Updated Sep 2, 2024
  • kde-rs Public
    COMBINE-lab/kde-rs’s past year of commit activity
    Rust 0 BSD-3-Clause 0 0 0 Updated Aug 31, 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 Aug 31, 2024
  • COMBINE-lab/combine-lab.github.io’s past year of commit activity
    HTML 8 5 0 1 Updated Aug 22, 2024
  • lr_quant_benchmarks Public

    A replicable and modular benchmark for long-read RNA transcript quantification methods

    COMBINE-lab/lr_quant_benchmarks’s past year of commit activity
    Python 5 BSD-3-Clause 1 1 1 Updated Aug 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++ 79 BSD-3-Clause 8 11 2 Updated Aug 10, 2024
  • radtk Public

    Various tools for working with RAD files

    COMBINE-lab/radtk’s past year of commit activity
    Rust 1 BSD-3-Clause 0 1 0 Updated Aug 5, 2024
  • COMBINE-lab/libradicl’s past year of commit activity
    Rust 1 BSD-3-Clause 2 0 0 Updated Aug 3, 2024

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