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    137 repositories

    • seqproc

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•4•1•Updated Apr 16, 2026Apr 16, 2026

    • simpleaf

      Public
      A rust framework to make using alevin-fry even simpler
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •6•64•17•0•Updated Apr 15, 2026Apr 15, 2026

    • piscem

      Public
      Mapping sequencing data to De Bruijn graphs, fast
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •3•32•2•0•Updated Apr 15, 2026Apr 15, 2026

    • piscem-rs

      Public
      Rust
      •1•5•0•0•Updated Apr 15, 2026Apr 15, 2026

    • sshash-rs

      Public
      A Rust implementation of SSHash
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•16•1•0•Updated Apr 15, 2026Apr 15, 2026

    • 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 barc…
      rustrna-seqquantification
      rustrna-seqquantificationtranscriptomicssingle-cell10xsingle-cell-rna-seq
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •20•203•24•0•Updated Apr 15, 2026Apr 15, 2026

    • piscem-infer

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•15•0•0•Updated Mar 27, 2026Mar 27, 2026

    • af-anndata

      Public
      alevin-fry related processing of AnnData
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•2•0•Updated Mar 23, 2026Mar 23, 2026

    • libradicl

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•1•0•Updated Mar 21, 2026Mar 21, 2026

    • grangers

      Public
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •2•19•0•0•Updated Mar 19, 2026Mar 19, 2026

    • oarfish

      Public
      long read RNA-seq quantification
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •8•109•11•2•Updated Mar 16, 2026Mar 16, 2026

    • salmon

      Public
      🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
      c-plus-plusbioinformaticsrna-seq
      c-plus-plusbioinformaticsrna-seqgene-expressionrnaseqscrna-seqquantificationtranscriptomesingle-cellquasi-mapping
      C++
      •
      GNU General Public License v3.0
      •184•876•384•3•Updated Mar 11, 2026Mar 11, 2026

    • pufferfish

      Public
      An efficient index for the colored, compacted, de Bruijn graph
      genomehashindex
      genomehashindexdebruijndbgcontigsdebruijn-graph
      C
      •
      GNU General Public License v3.0
      •22•112•24•3•Updated Mar 11, 2026Mar 11, 2026

    • wfa2lib-rs

      Public
      A rust-native port of wfa2lib
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•10•0•0•Updated Mar 9, 2026Mar 9, 2026

    • libgff

      Public
      C++
      •0•2•0•0•Updated Mar 6, 2026Mar 6, 2026

    • mim

      Public
      A small, auxiliary index to massively improve parallel fastq parsing
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •1•31•6•0•Updated Mar 6, 2026Mar 6, 2026

    • ksw2rs

      Public
      a native rust port of the KSW2 alignment procedure
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 2, 2026Mar 2, 2026

    • cf1-rs

      Public
      An subset of Cuttlefish 1, rewritten in Rust, to provide maximal unitigs and tiling information for piscem indexing.
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Feb 27, 2026Feb 27, 2026

    • cuttlefish

      Public
      Building the compacted de Bruijn graph efficiently from references or reads.
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •12•91•19•1•Updated Feb 26, 2026Feb 26, 2026

    • QCatch

      Public
      Quality Control downstream of alevin-fry / simpleaf
      Python
      •
      Other
      •2•6•0•2•Updated Feb 24, 2026Feb 24, 2026

    • file-requirements

      Public
      build up collections of files to check their existence
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 21, 2026Feb 21, 2026

    • OUP-Bioinformatics-Typst

      Public
      Unofficial attempt at a Typst template for the Oxford Bioinformatics journal
      Typst
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Feb 20, 2026Feb 20, 2026

    • ANTISEQUENCE

      Public
      Rust library for processing sequencing reads.
      Rust
      •
      MIT License
      •4•0•0•0•Updated Feb 19, 2026Feb 19, 2026

    • bsuccinct-rs

      Public
      Rust libraries and programs focused on succinct data structures
      Rust
      •
      Apache License 2.0
      •15•0•0•0•Updated Feb 16, 2026Feb 16, 2026

    • combine-lab.github.io

      Public
      HTML
      •15•13•1•1•Updated Feb 16, 2026Feb 16, 2026

    • piscem-cpp

      Public
      A small sparse and fast reference index based on SSHash and Tiling encoding
      C
      •
      MIT License
      •1•6•0•1•Updated Feb 14, 2026Feb 14, 2026

    • prep_reads

      Public
      simple and dirty internal tool for putting simulated reads into the right format for downstream consumption
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 17, 2026Jan 17, 2026

    • pipfp-rs

      Public
      A Rust implementation of pipfp
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • file-format-perspective

      Public
      TeX
      •
      MIT License
      •0•0•0•0•Updated Aug 15, 2025Aug 15, 2025

    • lr_quant_benchmarks

      Public
      A replicable and modular benchmark for long-read RNA transcript quantification methods
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•1•1•Updated Jul 8, 2025Jul 8, 2025
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