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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++ 866 185

  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 105 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 137 repositories
  • salmon Public

    🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

    COMBINE-lab/salmon’s past year of commit activity
    C++ 866 GPL-3.0 185 384 3 Updated Mar 7, 2026
  • pufferfish Public

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

    COMBINE-lab/pufferfish’s past year of commit activity
    C 111 GPL-3.0 22 24 3 Updated Mar 7, 2026
  • wfa2lib-rs Public

    A rust-native port of wfa2lib

    COMBINE-lab/wfa2lib-rs’s past year of commit activity
    Rust 2 BSD-3-Clause 0 0 0 Updated Mar 7, 2026
  • libgff Public
    COMBINE-lab/libgff’s past year of commit activity
    C++ 2 0 0 0 Updated Mar 6, 2026
  • mim Public

    A small, auxiliary index to massively improve parallel fastq parsing

    COMBINE-lab/mim’s past year of commit activity
    Rust 31 BSD-3-Clause 1 6 0 Updated Mar 6, 2026
  • ksw2rs Public

    a native rust port of the KSW2 alignment procedure

    COMBINE-lab/ksw2rs’s past year of commit activity
    Rust 1 BSD-3-Clause 0 0 0 Updated Mar 2, 2026
  • piscem Public

    Mapping sequencing data to De Bruijn graphs, fast

    COMBINE-lab/piscem’s past year of commit activity
    Rust 30 BSD-3-Clause 2 3 0 Updated Feb 28, 2026
  • cf1-rs Public

    An subset of Cuttlefish 1, rewritten in Rust, to provide maximal unitigs and tiling information for piscem indexing.

    COMBINE-lab/cf1-rs’s past year of commit activity
    Rust 1 BSD-3-Clause 0 0 0 Updated Feb 27, 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 26, 2026
  • 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

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