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    47 repositories

    • sahara

      Public
      Approximate Pattern Matching with Search Schemes
      C++
      •0•0•0•1•Updated Nov 6, 2024Nov 6, 2024

    • needle

      Public
      A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences
      bloom-filtersminimizerngs-dataibfseqan3
      C++
      •
      Other
      •6•14•7•2•Updated Nov 5, 2024Nov 5, 2024

    • hibf

      Public
      HIBF and IBF
      C++
      •
      Other
      •2•4•5•6•Updated Nov 4, 2024Nov 4, 2024

    • raptor

      Public
      A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
      filterbloom-filterthresholdbinningk-merminimizerset-membership
      C++
      •
      Other
      •18•52•8•3•Updated Nov 2, 2024Nov 2, 2024

    • chopper

      Public
      A tool for partitioning a set of sequences into similar batches.
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •9•9•6•2•Updated Nov 2, 2024Nov 2, 2024

    • seqan3

      Public
      The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
      bioinformaticsmodernfastablastseqanfastqsamtoolssequence-alignmentfm-indexsequence-analysis
      C++
      •
      Other
      •82•409•29•1•Updated Oct 30, 2024Oct 30, 2024

    • actions

      Public
      Shell
      •
      Creative Commons Attribution 4.0 International
      •2•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • sharg-parser

      Public
      The modern argument parser for c++ tools
      cppmodern-cppargument-parsingcommand-line-parsercpp20
      C++
      •
      Other
      •7•10•15•5•Updated Sep 23, 2024Sep 23, 2024

    • app-template

      Public template
      This template comes pre-configured with various SeqAn libraries and a basic Continuous Integration setup. It is designed to provide a robust starting point for your projects, while offering the flexibility to customize and adapt to your specific requirements.
      CMake
      •
      Other
      •9•6•19•0•Updated Sep 9, 2024Sep 9, 2024

    • www.seqan.de

      Public
      SCSS
      •
      MIT License
      •9•0•2•1•Updated Aug 28, 2024Aug 28, 2024

    • lambda

      Public
      LAMBDA – the Local Aligner for Massive Biological DatA
      bioinformaticshigh-performancemetagenomicsalignmentprotein-sequencesncbi-taxonomyblastblast-searchesseqan
      C++
      •
      Other
      •20•77•2•1•Updated Aug 26, 2024Aug 26, 2024

    • seqan

      Public
      SeqAn's official repository.
      high-performancecpp14indexingsimdalignmentbwtfastablastfastq-formatbioinfomatics
      C++
      •
      Other
      •171•481•104•4•Updated Aug 16, 2024Aug 16, 2024

    • hibf_benchmarks

      Public
      WIP HIBF benchmarks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•2•Updated Aug 13, 2024Aug 13, 2024

    • stellar3

      Public
      the SwifT Exact LocaL AligneR
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•1•Updated Aug 5, 2024Aug 5, 2024

    • ScavengerHunt

      Public
      Unix Scavenger Hunt
      Shell
      •4•0•0•0•Updated Jul 8, 2024Jul 8, 2024

    • seqan-std

      Public
      Implementation of several C++23 views
      C++
      •
      Other
      •2•0•0•0•Updated Jul 2, 2024Jul 2, 2024

    • cmake-scripts

      Public
      CMake
      •1•0•0•0•Updated Mar 13, 2024Mar 13, 2024

    • lemon

      Public
      Clone of the latest release of the lemon library (only the headers)
      C++
      •
      Other
      •2•5•0•0•Updated Sep 8, 2023Sep 8, 2023

    • minions

      Public
      Comparison between different methods to simplify sequence data
      k-merminimizerset-membership
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•8•0•Updated Aug 24, 2023Aug 24, 2023

    • mason

      Public
      Tools for Biological Sequence Simulation
      HTML
      •
      Other
      •2•2•0•2•Updated May 17, 2023May 17, 2023

    • flexbar

      Public
      flexible barcode and adapter removal
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •29•76•19•1•Updated Feb 10, 2023Feb 10, 2023

    • library-template

      Public template
      WIP
      CMake
      •
      Other
      •1•1•0•0•Updated Feb 8, 2023Feb 8, 2023

    • io-playground

      Public
      WIP
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 20, 2023Jan 20, 2023

    • iGenVar

      Public
      The official repository for the iGenVar project.
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •8•9•33•4•Updated Nov 23, 2022Nov 23, 2022

    • seqan3-infrastructure

      Public
      Infrastructure for seqan3 including nightly builds, continues integration, continues deployment, coverage tests, static code analysis and containerisation.
      CMake
      •2•1•0•0•Updated Oct 9, 2022Oct 9, 2022

    • mars

      Public
      Motif-based aligned RNA searcher
      motifrna-structuredescriptors
      C++
      •
      Other
      •2•0•0•0•Updated Aug 11, 2022Aug 11, 2022

    • vaquita

      Public
      Identification of structural variations
      C++
      •
      Other
      •4•12•9•2•Updated Jul 22, 2022Jul 22, 2022

    • range-v3

      Public archive
      Range library for C++14/17/20, basis for C++20's std::ranges
      C++
      •
      Other
      •439•0•0•0•Updated Jun 8, 2022Jun 8, 2022

    • lara

      Public
      LaRA 2: Lagrangian Relaxed structural Alignment
      bioinformaticsalignmentrna-structurerna
      C++
      •
      Other
      •3•4•1•0•Updated Nov 4, 2021Nov 4, 2021

    • learning-resources

      Public
      Provides online material and tutorials for modern C++, efficient data structures and algorithms.
      C++
      •
      Other
      •6•6•0•0•Updated Sep 14, 2021Sep 14, 2021